From 4a247fc7232a522d354734a1169c18184fc92933 Mon Sep 17 00:00:00 2001 From: sbabyanusha Date: Mon, 10 Apr 2023 19:37:05 -0400 Subject: [PATCH 1/5] Added genetic ancestry data for all TCGA PANCAN studies --- .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ .../data_clinical_patient.txt | 4 ++-- .../data_genetic_ancestry.txt | 3 +++ .../meta_genetic_ancestry.txt | 11 +++++++++++ 93 files changed, 496 insertions(+), 62 deletions(-) create mode 100644 public/acc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/acc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/blca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/blca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/brca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/brca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/cesc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/cesc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/chol_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/chol_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/coadread_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/coadread_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/dlbc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/dlbc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/esca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/esca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/gbm_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/gbm_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/hnsc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/hnsc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/kich_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/kich_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/kirc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/kirc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/kirp_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/kirp_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/lgg_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/lgg_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/lihc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/lihc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/luad_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/luad_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/lusc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/lusc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/meso_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/meso_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/ov_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/ov_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/paad_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/paad_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/pcpg_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/pcpg_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/prad_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/prad_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/sarc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/sarc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/skcm_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/skcm_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/stad_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/stad_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/tgct_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/tgct_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/thca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/thca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/thym_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/thym_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/ucec_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/ucec_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/ucs_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/ucs_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt create mode 100644 public/uvm_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt create mode 100644 public/uvm_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt diff --git a/public/acc_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/acc_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 4a538ec05e..949cf4fdf9 100644 --- a/public/acc_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/acc_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:17c2a306a7fdcb36455c89c74b9ab5ccb697cfa7adfc1c0913709870ebddb338 -size 31230 +oid sha256:3fd603b49d1560ebbc8fb241b04250cdeffeed60197fd3ccdeacfda8e7257d4f +size 31688 diff --git a/public/acc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/acc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..78d5b0c85b --- /dev/null +++ b/public/acc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:81d2c1d1ed898f1bae57f3c7bde1b8689b145e34de226ccdda6bf5d738d4180f +size 5382 diff --git a/public/acc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/acc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..f3e310baa8 --- /dev/null +++ b/public/acc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: acc_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Admixture percentage by samples. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC \ No newline at end of file diff --git a/public/blca_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/blca_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 8dec57ed7e..725d03ebee 100644 --- a/public/blca_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/blca_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:1f4c60d42bea0966f5a72e76e3e25ea4af41a59a8a16b9538c0a02a6e0bbce57 -size 125317 +oid sha256:112c38fd0ab3df68ceda82eec24bcdf10d7cf6622da4622bc1dbdc162ff69d5d +size 126963 diff --git a/public/blca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/blca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..c699e68214 --- /dev/null +++ b/public/blca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0e827efe98f6fb1fadae5361bcb77b223c41f03f7e199b9505d7ebb7c9ee1d59 +size 23759 diff --git a/public/blca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/blca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..0a2073f306 --- /dev/null +++ b/public/blca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: blca_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC diff --git a/public/brca_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/brca_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 849f85d623..b4acfd0825 100644 --- a/public/brca_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/brca_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:10392d88e2b9077fffcb9e649276455aa1740ba22cc14d887848fce3b7183550 -size 337168 +oid sha256:c6c49d1858b2c07d93d2552c889e8fd8b519f1140ca57f774356d49f383571c9 +size 341638 diff --git a/public/brca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/brca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..ed2ef3eb4e --- /dev/null +++ b/public/brca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:34529dd0fcd2b06215d93f28acf8191c9a17364e145c43cadf45ad2727c5abcb +size 62835 diff --git a/public/brca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/brca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..e007daa0b6 --- /dev/null +++ b/public/brca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: brca_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC diff --git a/public/cesc_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/cesc_tcga_pan_can_atlas_2018/data_clinical_patient.txt index d6fbc62148..fbe32f488b 100644 --- a/public/cesc_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/cesc_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:842b8b92e2c70c8e27a827e428d19e04e4cb257e609609f546d6c15f98d41dc6 -size 93965 +oid sha256:cf308dd0c06722a4b3142d5da89d9ecc323c82dd2437284b13792484a29f3fb8 +size 95319 diff --git a/public/cesc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/cesc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..c1e2114db8 --- /dev/null +++ b/public/cesc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:42d1bcd8d2331fb9487b5c2b26370b7f89e8a93a2568209e83bfd6e6f343c9c7 +size 16783 diff --git a/public/cesc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/cesc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..f1d5e6d480 --- /dev/null +++ b/public/cesc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: cesc_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC diff --git a/public/chol_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/chol_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 9714be06f3..7c79e9a973 100644 --- a/public/chol_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/chol_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:021576354b417bf2a7e54b25a3da20337b8cbf3e77351d6afdd7c28e37629a38 -size 16722 +oid sha256:e4c8665184edbb3d1b7afa9c906cca32cab64af769bd5579e1b6f86030f06923 +size 16946 diff --git a/public/chol_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/chol_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..3fa7c01a8f --- /dev/null +++ b/public/chol_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a1f4596e1794679ab5e7e43bb99359479b3ea0dbb5b78c860a86c4186401ef6e +size 2301 diff --git a/public/chol_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/chol_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..bad1652fe2 --- /dev/null +++ b/public/chol_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: chol_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC \ No newline at end of file diff --git a/public/coadread_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/coadread_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 9cf1ebe2d0..dddb1d4d8e 100644 --- a/public/coadread_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/coadread_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:0d03471199372e0f43dea0e271c26a8aa9d00bc70a276ccb8c9f580a7adc988e -size 172415 +oid sha256:c19f9f91f47db6a48d250c8a6c59a8c5068a1e20c9798083a41de81d48630d3d +size 175005 diff --git a/public/coadread_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/coadread_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..1de5a28860 --- /dev/null +++ b/public/coadread_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:84e74a885e149dd4150ffc56a6186cf6eb91f5711bc3defed346e34908d4f78b +size 33217 diff --git a/public/coadread_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/coadread_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..f76f51d56e --- /dev/null +++ b/public/coadread_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: coadread_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. 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The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC diff --git a/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 70d65b30a7..2b2d693485 100644 --- a/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:5a5d8b4776704bf66b2f8e8a1804db47da98ba455dd0ae721974bc66fbd12c41 -size 156380 +oid sha256:77490263dbe04ec3299f7e524d409f991f95af6e8ee4089918a23140a0d0d743 +size 161180 diff --git a/public/hnsc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/hnsc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..49434638e3 --- /dev/null +++ b/public/hnsc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f3b1a1bcc613bf5cad64c202dd876a1856ecee89940f0b1b00cddd65698d5d47 +size 29910 diff --git a/public/hnsc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/hnsc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..4baf167e51 --- /dev/null +++ b/public/hnsc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). 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The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC \ No newline at end of file diff --git a/public/tgct_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/tgct_tcga_pan_can_atlas_2018/data_clinical_patient.txt index bd757ce2b6..9621b9e059 100644 --- a/public/tgct_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/tgct_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d298a6d5fd97145c4fe599d5fa88822c4b1d120711d60356ee0b81b0ffe9ae45 -size 47986 +oid sha256:527105f28d74dbe7b85deb30a111e25a57d44f2697a7c8bcb94d9223d3213ae0 +size 48644 diff --git a/public/tgct_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/tgct_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..f7a958c0ee --- /dev/null +++ b/public/tgct_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bbc30372ba40ebb0e92c0403a494c325564a95e4804b88f2dfbb9e63ae6f4993 +size 9088 diff --git a/public/tgct_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/tgct_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..080ec40b6e --- /dev/null +++ b/public/tgct_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: tgct_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC diff --git a/public/thca_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/thca_tcga_pan_can_atlas_2018/data_clinical_patient.txt index e8f73c7e98..0b2663ad89 100644 --- a/public/thca_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/thca_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:6eebf0f4acf982757f8f8c7a687e80cf89668107b73fa2e344442de1474b055f -size 151468 +oid sha256:7bc7060ad300f81b15f3f7498875836327957ff211158beb9b35e5bca38a4e9f +size 153576 diff --git a/public/thca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/thca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..99d22fc032 --- /dev/null +++ b/public/thca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ec31d153b58f3f32e50e657de4864f07a2f546e8932f5c08c29f2e1c3c761cf8 +size 28722 diff --git a/public/thca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/thca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..ebe5ac3492 --- /dev/null +++ b/public/thca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: thca_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC \ No newline at end of file diff --git a/public/thym_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/thym_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 55cc426952..a10fe36306 100644 --- a/public/thym_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/thym_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:cb092950164553d4947b9911485a52196793c1e49c244599b5b46fd2b5ae64b6 -size 37199 +oid sha256:7b5029864c6ef6f7692631ecfde80338933659bd5b4aa873b324fe4574e151a8 +size 37803 diff --git a/public/thym_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/thym_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..fae7beea13 --- /dev/null +++ b/public/thym_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:58a602997f20408a1272418f9f5220052a352fb6778fe465789e3d983af88826 +size 7584 diff --git a/public/thym_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/thym_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..34399ec417 --- /dev/null +++ b/public/thym_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: thym_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC diff --git a/public/ucec_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/ucec_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 893b144f3a..7c5659d5ae 100644 --- a/public/ucec_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/ucec_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:0302d14fc6042a73238aabd58f2e9aeb1b346be9a2ad44c121f1c5ebea2e1bf1 -size 159554 +oid sha256:e182af26e936a0bc3b4770b5c93fe83136388c3748bd7ee180f002857c8eb197 +size 162533 diff --git a/public/ucec_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/ucec_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..bf39803b1b --- /dev/null +++ b/public/ucec_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bc5f3321d897b008594b8c5d7c5f8c2b6069e8aa2e8968f6d0728236e03363d6 +size 30146 diff --git a/public/ucec_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/ucec_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..7cf4b0fb0f --- /dev/null +++ b/public/ucec_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: ucec_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC \ No newline at end of file diff --git a/public/ucs_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/ucs_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 87c651267c..0dc631a306 100644 --- a/public/ucs_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/ucs_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:2f02ea520d664443151145270343664792b3fa0b310877ee04eee3b1c34ce764 -size 17732 +oid sha256:31bf693c570fd24f4a8f3fc9be028ddaa3716a82714cbcfe2a38edfd16caaba3 +size 18147 diff --git a/public/ucs_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/ucs_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..56043bbb35 --- /dev/null +++ b/public/ucs_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7cbed9f3803b2d888a1add155d1cb80f1a4afa01801ef90a5d6f6b54db8381d8 +size 3449 diff --git a/public/ucs_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/ucs_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..651a6149da --- /dev/null +++ b/public/ucs_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: ucs_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC \ No newline at end of file diff --git a/public/uvm_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/uvm_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 13b08918b1..52a74bc62a 100644 --- a/public/uvm_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/uvm_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:37ce810b598d74c4890cf3c32698eca3e10b5dfc67fd1e7759bb5a549a05782b -size 16814 +oid sha256:0190a1d17448551feaedd6d51b2f440f57492d2846b790aba96c77dcdea777a8 +size 17318 diff --git a/public/uvm_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/uvm_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..7538dc2ab3 --- /dev/null +++ b/public/uvm_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b977e615ce33667d9d38781f528ca0d23cdd66e47913f14bb1b9c398116456d2 +size 4915 diff --git a/public/uvm_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/uvm_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..c5c10bad19 --- /dev/null +++ b/public/uvm_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: uvm_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC \ No newline at end of file From f6e9daad582035f02f32314ee5c05ceda70afc9b Mon Sep 17 00:00:00 2001 From: sbabyanusha Date: Tue, 11 Apr 2023 09:53:10 -0400 Subject: [PATCH 2/5] Added genetic ancestry data for all TCGA PANCAN studies --- public/acc_tcga_pan_can_atlas_2018/data_clinical_patient.txt | 2 +- public/acc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt | 2 +- public/acc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt | 5 ++--- .../hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt | 4 ++-- .../luad_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt | 4 ++-- 5 files changed, 8 insertions(+), 9 deletions(-) diff --git a/public/acc_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/acc_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 949cf4fdf9..d8087225bb 100644 --- a/public/acc_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/acc_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:3fd603b49d1560ebbc8fb241b04250cdeffeed60197fd3ccdeacfda8e7257d4f +oid sha256:3e9338f0d969fa5174c5575dee2d9e3627252e8277ca013c0bbc6d579e66c671 size 31688 diff --git a/public/acc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/acc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt index 78d5b0c85b..6db7fc88a5 100644 --- a/public/acc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt +++ b/public/acc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:81d2c1d1ed898f1bae57f3c7bde1b8689b145e34de226ccdda6bf5d738d4180f +oid sha256:50c4c53dcdede6926d138ed4cee7a77ed6a47fa48ffc2c3d5d057730478b9e07 size 5382 diff --git a/public/acc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/acc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt index f3e310baa8..efc59f6a52 100644 --- a/public/acc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt +++ b/public/acc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -1,11 +1,10 @@ cancer_study_identifier: acc_tcga_pan_can_atlas_2018 genetic_alteration_type: GENERIC_ASSAY -generic_assay_type: GENETIC_ANCESTRY +generic_assay_type: ARMLEVEL_CNA datatype: LIMIT-VALUE stable_id: genetic_ancestry profile_name: Genetic Ancestry -profile_description: Admixture percentage by samples. +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. data_filename: data_genetic_ancestry.txt show_profile_in_analysis_tab: true generic_entity_meta_properties: NAME -value_sort_order: ASC \ No newline at end of file diff --git a/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 2b2d693485..994e938dde 100644 --- a/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:77490263dbe04ec3299f7e524d409f991f95af6e8ee4089918a23140a0d0d743 -size 161180 +oid sha256:f319983b74e63894ca06afee8b4246b0010aa2f4e0e346bb272017bef8a55fa6 +size 161146 diff --git a/public/luad_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/luad_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt index 4697da792d..89d2585ad8 100644 --- a/public/luad_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt +++ b/public/luad_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:17e5f52d261c7c6577b59ffbd10ec06350d216f3730a30b5125789fc917118b5 -size 29964 +oid sha256:9472a37e6087cfdeb6712c6d9854221fc2c67a385ec2a2d6f8498145746b607a +size 29904 From 9b2cd6ff3da6888874a9924204a3e88d163da5b1 Mon Sep 17 00:00:00 2001 From: sbabyanusha Date: Tue, 11 Apr 2023 12:25:28 -0400 Subject: [PATCH 3/5] Fix error --- public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 994e938dde..b92108ddcc 100644 --- a/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:f319983b74e63894ca06afee8b4246b0010aa2f4e0e346bb272017bef8a55fa6 -size 161146 +oid sha256:10e6eefdf38c9fd3bd5eb160535619c54a519fb86d0eca99d708f342dd23024f +size 158624 From 5f7cac65c7afd30a3770b190cb33719611a76551 Mon Sep 17 00:00:00 2001 From: sbabyanusha Date: Tue, 27 Jun 2023 14:03:57 -0400 Subject: [PATCH 4/5] Updated readme --- public/acc_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/blca_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/brca_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/cesc_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/chol_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- .../README.md | 20 ++++++++++++++++++- public/dlbc_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/esca_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/gbm_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/hnsc_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/kich_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/kirc_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/kirp_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/laml_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/lgg_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/lihc_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/luad_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/lusc_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/meso_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/ov_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/paad_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/pcpg_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/prad_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/sarc_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/skcm_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/stad_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/tgct_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/thca_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/thym_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/ucec_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/ucs_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- public/uvm_tcga_pan_can_atlas_2018/README.md | 20 ++++++++++++++++++- 32 files changed, 608 insertions(+), 32 deletions(-) diff --git a/public/acc_tcga_pan_can_atlas_2018/README.md b/public/acc_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/acc_tcga_pan_can_atlas_2018/README.md +++ b/public/acc_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/blca_tcga_pan_can_atlas_2018/README.md b/public/blca_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/blca_tcga_pan_can_atlas_2018/README.md +++ b/public/blca_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/brca_tcga_pan_can_atlas_2018/README.md b/public/brca_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/brca_tcga_pan_can_atlas_2018/README.md +++ b/public/brca_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/cesc_tcga_pan_can_atlas_2018/README.md b/public/cesc_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/cesc_tcga_pan_can_atlas_2018/README.md +++ b/public/cesc_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/chol_tcga_pan_can_atlas_2018/README.md b/public/chol_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/chol_tcga_pan_can_atlas_2018/README.md +++ b/public/chol_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/coadread_tcga_pan_can_atlas_2018/README.md b/public/coadread_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/coadread_tcga_pan_can_atlas_2018/README.md +++ b/public/coadread_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/dlbc_tcga_pan_can_atlas_2018/README.md b/public/dlbc_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/dlbc_tcga_pan_can_atlas_2018/README.md +++ b/public/dlbc_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/esca_tcga_pan_can_atlas_2018/README.md b/public/esca_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/esca_tcga_pan_can_atlas_2018/README.md +++ b/public/esca_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/gbm_tcga_pan_can_atlas_2018/README.md b/public/gbm_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/gbm_tcga_pan_can_atlas_2018/README.md +++ b/public/gbm_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/hnsc_tcga_pan_can_atlas_2018/README.md b/public/hnsc_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/hnsc_tcga_pan_can_atlas_2018/README.md +++ b/public/hnsc_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/kich_tcga_pan_can_atlas_2018/README.md b/public/kich_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/kich_tcga_pan_can_atlas_2018/README.md +++ b/public/kich_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/kirc_tcga_pan_can_atlas_2018/README.md b/public/kirc_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/kirc_tcga_pan_can_atlas_2018/README.md +++ b/public/kirc_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/kirp_tcga_pan_can_atlas_2018/README.md b/public/kirp_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/kirp_tcga_pan_can_atlas_2018/README.md +++ b/public/kirp_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/laml_tcga_pan_can_atlas_2018/README.md b/public/laml_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/laml_tcga_pan_can_atlas_2018/README.md +++ b/public/laml_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/lgg_tcga_pan_can_atlas_2018/README.md b/public/lgg_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/lgg_tcga_pan_can_atlas_2018/README.md +++ b/public/lgg_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/lihc_tcga_pan_can_atlas_2018/README.md b/public/lihc_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/lihc_tcga_pan_can_atlas_2018/README.md +++ b/public/lihc_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/luad_tcga_pan_can_atlas_2018/README.md b/public/luad_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/luad_tcga_pan_can_atlas_2018/README.md +++ b/public/luad_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/lusc_tcga_pan_can_atlas_2018/README.md b/public/lusc_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/lusc_tcga_pan_can_atlas_2018/README.md +++ b/public/lusc_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/meso_tcga_pan_can_atlas_2018/README.md b/public/meso_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/meso_tcga_pan_can_atlas_2018/README.md +++ b/public/meso_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/ov_tcga_pan_can_atlas_2018/README.md b/public/ov_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/ov_tcga_pan_can_atlas_2018/README.md +++ b/public/ov_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/paad_tcga_pan_can_atlas_2018/README.md b/public/paad_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/paad_tcga_pan_can_atlas_2018/README.md +++ b/public/paad_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/pcpg_tcga_pan_can_atlas_2018/README.md b/public/pcpg_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/pcpg_tcga_pan_can_atlas_2018/README.md +++ b/public/pcpg_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/prad_tcga_pan_can_atlas_2018/README.md b/public/prad_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/prad_tcga_pan_can_atlas_2018/README.md +++ b/public/prad_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/sarc_tcga_pan_can_atlas_2018/README.md b/public/sarc_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/sarc_tcga_pan_can_atlas_2018/README.md +++ b/public/sarc_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/skcm_tcga_pan_can_atlas_2018/README.md b/public/skcm_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/skcm_tcga_pan_can_atlas_2018/README.md +++ b/public/skcm_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/stad_tcga_pan_can_atlas_2018/README.md b/public/stad_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/stad_tcga_pan_can_atlas_2018/README.md +++ b/public/stad_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/tgct_tcga_pan_can_atlas_2018/README.md b/public/tgct_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/tgct_tcga_pan_can_atlas_2018/README.md +++ b/public/tgct_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/thca_tcga_pan_can_atlas_2018/README.md b/public/thca_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/thca_tcga_pan_can_atlas_2018/README.md +++ b/public/thca_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/thym_tcga_pan_can_atlas_2018/README.md b/public/thym_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/thym_tcga_pan_can_atlas_2018/README.md +++ b/public/thym_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/ucec_tcga_pan_can_atlas_2018/README.md b/public/ucec_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/ucec_tcga_pan_can_atlas_2018/README.md +++ b/public/ucec_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/ucs_tcga_pan_can_atlas_2018/README.md b/public/ucs_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/ucs_tcga_pan_can_atlas_2018/README.md +++ b/public/ucs_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/uvm_tcga_pan_can_atlas_2018/README.md b/public/uvm_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/uvm_tcga_pan_can_atlas_2018/README.md +++ b/public/uvm_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file From fb833f2b819cf62a65be53ec533867c83a3872cf Mon Sep 17 00:00:00 2001 From: Gaofei Zhao <15748980+dippindots@users.noreply.github.com> Date: Wed, 9 Aug 2023 17:52:03 -0400 Subject: [PATCH 5/5] Update tests --- .circleci/config.yml | 23 ----------------- .../workflows/validate_changed_studies.yml | 25 +++++++++++++++++++ 2 files changed, 25 insertions(+), 23 deletions(-) create mode 100644 .github/workflows/validate_changed_studies.yml diff --git a/.circleci/config.yml b/.circleci/config.yml index 2e446a922e..261affa968 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -4,25 +4,6 @@ # version: 2 jobs: - - # Job to validate only the changed studies - build: - docker: - - image: circleci/python:3.6 - resource_class: large - working_directory: ~/repo/ - steps: - - checkout - - run: - name: Validate changed studies - command: | - cd ~/repo/.circleci - ./install_dependencies.sh - ./validate_changed_studies.sh - no_output_timeout: 2h - - store_artifacts: - path: ~/test-reports - destination: ~/test-reports # Job to validate all studies validate_all_studies: @@ -92,10 +73,6 @@ workflows: # is merged into the master branch. workflow_on_commit: jobs: - - build: - filters: - branches: - ignore: master - validate_changed_seed: filters: branches: diff --git a/.github/workflows/validate_changed_studies.yml b/.github/workflows/validate_changed_studies.yml new file mode 100644 index 0000000000..aa597452f9 --- /dev/null +++ b/.github/workflows/validate_changed_studies.yml @@ -0,0 +1,25 @@ +name: Validate Changed Studies + +on: + pull_request: + branches: + - master + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v2 + + - name: Configure Git + run: | + git config user.name "Continuous Integration" + git config user.email "ci@example.com" + + - name: Validate changed studies + run: | + cd .circleci + ./install_dependencies.sh + ./validate_changed_studies.sh