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    42 repositories

    • easyquant

      Public
      Quantification of reads at defined positions to verify custom input sequences.
      Python
      •
      MIT License
      •0•3•2•0•Updated Oct 23, 2024Oct 23, 2024

    • snakemake-wrappers

      Public
      This is the development home of the Snakemake wrapper repository, see
      Python
      •186•0•0•0•Updated Oct 16, 2024Oct 16, 2024

    • mavis-bench

      Public
      Merging, Annotation, Validation, and Illustration of Structural variants
      Python
      •
      GNU General Public License v3.0
      •14•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • nf-template

      Public template
      Nextflow template for fast pipeline generation
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

    • EasyFuse

      Public
      EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
      Python
      •
      GNU General Public License v3.0
      •13•49•13•1•Updated Aug 26, 2024Aug 26, 2024

    • covigator

      Public
      CoVigator - Monitoring SARS-CoV-2 mutations
      dashboarddashcoronaviruscovid-19sars-cov-2bioinformatics
      Python
      •
      MIT License
      •1•11•6•3•Updated Aug 2, 2024Aug 2, 2024

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.3k•0•0•0•Updated Aug 1, 2024Aug 1, 2024

    • neofox

      Public
      Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors
      immunogenomicsimmunogenicity-predictioncancer-immunologynetmhciipannetmhcpanneoantigen-annotationneoantigensbioinformatics
      Python
      •
      GNU General Public License v3.0
      •6•27•4•0•Updated Jul 31, 2024Jul 31, 2024

    • splice2neo

      Public
      R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes
      R
      •
      Other
      •1•13•1•0•Updated Jul 23, 2024Jul 23, 2024

    • tronflow-alignment

      Public
      Nextflow pipeline for BWA, BWA2 and STAR alignments
      bwatronflowbioinformaticsrna-seqngs
      Nextflow
      •
      MIT License
      •3•12•0•1•Updated Jul 22, 2024Jul 22, 2024

    • covigator-ngs-pipeline

      Public
      A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.
      nextflowvariant-callerscoronaviruscovid-19sars-cov-2bioinformaticsgenomicsngs
      Nextflow
      •
      MIT License
      •7•18•5•2•Updated Jul 11, 2024Jul 11, 2024

    • tronflow-bam-preprocessing

      Public
      Nextflow pipeline for the preprocessing of BAM files based on GATK best practices. Marking duplicates, realignment around indels, base quality score recalibration (BQSR) and reporting of metrics are optional to maintain flexibility for different use cases.
      picardbioinformaticsnextflowgatktronflow
      Nextflow
      •
      MIT License
      •0•5•4•1•Updated Jul 4, 2024Jul 4, 2024

    • tronflow-hla-hd

      Public
      A Nextflow workflow for HLA typing using HLA-HD
      hla-typingbioinformatics
      Nextflow
      •
      MIT License
      •0•6•0•0•Updated Jul 3, 2024Jul 3, 2024

    • tronflow-vcf-postprocessing

      Public
      A Nextflow variant normalization pipeline based on vt and bcftools
      bioinformaticsnextflowvtbcftoolsnormalizing-variantstronflowvcf
      Shell
      •
      MIT License
      •1•5•1•0•Updated Jul 1, 2024Jul 1, 2024

    • tronflow-mutect2

      Public
      Nextflow pipeline for Mutect2 somatic variant calling best practices
      nextflowmutect2tronflowbioinformatics
      Nextflow
      •
      MIT License
      •3•21•2•2•Updated Jun 14, 2024Jun 14, 2024

    • tronflow-copy-number-calling

      Public
      A nextflow workflow for copy number calling
      cnvbioinformatics
      Nextflow
      •
      MIT License
      •0•1•0•1•Updated Jun 11, 2024Jun 11, 2024

    • curahack

      Public
      MIT License
      •0•0•0•0•Updated Apr 25, 2024Apr 25, 2024

    • env2sif

      Public
      Python script for creating and editing Singularity images on a HPC servers without sudo rights.
      Python
      •
      Other
      •0•0•1•0•Updated Apr 11, 2024Apr 11, 2024

    • splicing_manuscript_scripts

      Public
      Scripts related to the manuscript "Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates"
      Shell
      •
      MIT License
      •0•1•0•0•Updated Mar 21, 2024Mar 21, 2024

    • TCLP

      Public
      an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression
      0•8•2•0•Updated Feb 26, 2024Feb 26, 2024

    • tronflow

      Public
      TronFlow documentation
      bioinformaticsnextflowtronflow
      Nextflow
      •0•1•0•1•Updated Oct 26, 2023Oct 26, 2023

    • seq2HLA

      Public
      In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.
      Python
      •
      MIT License
      •7•46•14•1•Updated Aug 24, 2023Aug 24, 2023

    • easyfuse-src

      Public
      EasyFuse source code to build python package
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 18, 2023Aug 18, 2023

    • milneo_analysis

      Public
      Code related to the manuscript "Multiple instance learning to predict immune checkpoint blockade efficacy using neoantigen candidates"
      R
      •0•1•0•0•Updated Aug 16, 2023Aug 16, 2023

    • nf-core-modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •696•1•0•0•Updated Jul 21, 2023Jul 21, 2023

    • variantmedium

      Public
      0•2•0•0•Updated Jul 17, 2023Jul 17, 2023

    • nf-core-test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •344•1•0•0•Updated Jul 11, 2023Jul 11, 2023

    • tronflow-test-data

      Public
      A collection of test data for our TronFlow pipelines
      testingdataci-cd
      0•1•0•0•Updated Jul 4, 2023Jul 4, 2023

    • covigator-analysis

      Public
      Some data analysis and prototypes from the CoVigator project
      Jupyter Notebook
      •0•0•0•0•Updated Jun 6, 2023Jun 6, 2023

    • covigator-intrahost-model

      Public
      0•0•0•0•Updated May 31, 2023May 31, 2023