From c981a05af55c6cbd1e797d37bcde40680ad6cd9d Mon Sep 17 00:00:00 2001 From: LeonStadelmann <169152764+LeonStadelmann@users.noreply.github.com> Date: Tue, 8 Oct 2024 08:26:06 +0200 Subject: [PATCH] Add link to pancreas dataset (#750) * Add link to pancreas dataset * Added pancreas dataset to docs * fixed citation + func ref --------- Co-authored-by: LeonStadelmann --- docs/user.rst | 1 + src/moscot/datasets.py | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/user.rst b/docs/user.rst index f4291892a..ccc769697 100644 --- a/docs/user.rst +++ b/docs/user.rst @@ -53,6 +53,7 @@ Datasets datasets.drosophila datasets.hspc datasets.mosta + datasets.pancreas_multiome datasets.sciplex datasets.sim_align datasets.simulate_data diff --git a/src/moscot/datasets.py b/src/moscot/datasets.py index 58c1c8870..1dc3c381f 100644 --- a/src/moscot/datasets.py +++ b/src/moscot/datasets.py @@ -281,11 +281,11 @@ def pancreas_multiome( force_download: bool = True, **kwargs: Any, ) -> Union[mu.MuData, ad.AnnData]: # pragma: no cover - """Pancreatic endocrinogenesis dataset published with the moscot manuscript :cite:`Klein:23`. + """Pancreatic endocrinogenesis dataset published with the moscot manuscript :cite:`klein:23`. The dataset contains paired scRNA-seq and scATAC-seq data of pancreatic cells at embryonic days 14.5, 15.5, and 16.5. The data was preprocessed and filtered as described in the manuscript, the raw data and the full processed - data are available via GEO accession code GSE275562. + data are available via `GEO `_ accession code GSE275562. Parameters ---------- @@ -296,7 +296,7 @@ def pancreas_multiome( force_download Whether to force-download the data. kwargs - Keyword arguments for :func:`anndata.read_h5ad` if `rna_only`, else for :func:`mudata.read`. + Keyword arguments for :func:`anndata.io.read_h5ad` if `rna_only`, else for :func:`mudata.read`. Returns -------