From 621dc9e29b4364d3abbc01af64e05246969e5305 Mon Sep 17 00:00:00 2001 From: "david.seb.fischer" Date: Wed, 14 Aug 2019 15:12:37 +0200 Subject: [PATCH 1/4] incremented batchglm version requirement --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index cb70fda..33da345 100644 --- a/setup.py +++ b/setup.py @@ -21,7 +21,7 @@ 'scipy', 'pandas', 'patsy>=0.5.0', - 'batchglm>=0.6.0', + 'batchglm>=0.6.1', 'xarray', 'statsmodels', ], From d33e20eae97a627525351c34c6aa3d49f848cbb5 Mon Sep 17 00:00:00 2001 From: "david.seb.fischer" Date: Wed, 14 Aug 2019 15:35:24 +0200 Subject: [PATCH 2/4] updated README to rst --- README.md | 20 -------------------- README.rst | 20 ++++++++++++++++++++ setup.py | 2 +- 3 files changed, 21 insertions(+), 21 deletions(-) delete mode 100644 README.md create mode 100644 README.rst diff --git a/README.md b/README.md deleted file mode 100644 index f9118ea..0000000 --- a/README.md +++ /dev/null @@ -1,20 +0,0 @@ -# Fast and scalable differential expression analysis on single-cell RNA-seq data -diffxpy covers a wide range of differential expression analysis scenarios encountered in single-cell RNA-seq scenarios. The core ideas of diffxpy is to speed up the model fitting time, which is the run-time bottle-neck of differential expression analysis on models that require maximum likelihood estimators and that do not have closed form solutions thereof. This model fitting is performed in a separate package, batchglm. diffxpy exposes wrapper funtions to the user which perform the model fitting and the differential expression test. Advanced users can chose the between various hypothesis tests and can vary the model fitting hyperparameters. Fitting can be performed both on CPUs and on GPUs and can be parallelized. - -# Worklows and API -Diffxpy supports workflows related to differential expression analysis. The functionalities of the workflows are structured in the API. To access these workflows, import diffxpy as follows `import diffxpy.api as de`. Currently, the following analytic strategies are implemented: - -1. differential expression analysis in `de.test.*` -2. gene set enrichment analysis based on differential expression calls in `de.enrich.*` - -The aforementioned workflows can be concatenated in pipelines and results can be shared via diffxpy data structures as explained in the individual functions and in the examples. -Refer to the documentation for details of the individual submodules. - -# Installation -Please refer to the [documentation](https://diffxpy.rtfd.io). - -# Tutorials -Please refer to the [documentation](https://diffxpy.rtfd.io). - -# Documentation -The documentation of diffxpy is hosted [here](https://diffxpy.rtfd.io). diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..4c13bcc --- /dev/null +++ b/README.rst @@ -0,0 +1,20 @@ +|PyPI| |Docs| + +.. |PyPI| image:: https://img.shields.io/pypi/v/diffxpy.svg + :target: https://pypi.org/project/diffxpy +.. |Docs| image:: https://readthedocs.com/projects/diffxpy/badge/?version=latest + :target: https://diffxpy.readthedocs.io + +# Fast and scalable differential expression analysis on single-cell RNA-seq data +diffxpy covers a wide range of differential expression analysis scenarios encountered in single-cell RNA-seq scenarios +and integrates into scanpy_ workflows. +Import diffxpy as `import diffxpy.api as de` to access the following differential expression analysis-related tools: + + 1. *differential expression analysis* in the module `de.test.*` + 2. *gene set enrichment analysis* based on differential expression calls in the module `de.enrich.*` + +Refer to the documentation_ and the tutorials_ for details of these modules. + +.. _scanpy: https://github.com/theislab/scanpy +.. _documentation: https://diffxpy.rtfd.io/en/latest +.. _tutorials: https://diffxpy.rtfd.io/en/latest/tutorials.html diff --git a/setup.py b/setup.py index 33da345..2f43452 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ author_email='david.fischer@helmholtz-muenchen.de, diffxpy@frhoelzlwimmer.de' description="Fast and scalable differential expression analysis on single-cell RNA-seq data" -with open("README.md", "r") as fh: +with open("README.rst", "r") as fh: long_description = fh.read() setup( From f0c4527f4b9c4444c1691ab5e09c3a4592c18d4a Mon Sep 17 00:00:00 2001 From: "david.seb.fischer" Date: Wed, 14 Aug 2019 15:37:11 +0200 Subject: [PATCH 3/4] attempted rst fix --- README.rst | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index 4c13bcc..befc50b 100644 --- a/README.rst +++ b/README.rst @@ -5,13 +5,15 @@ .. |Docs| image:: https://readthedocs.com/projects/diffxpy/badge/?version=latest :target: https://diffxpy.readthedocs.io -# Fast and scalable differential expression analysis on single-cell RNA-seq data +Fast and scalable differential expression analysis on single-cell RNA-seq data +=== + diffxpy covers a wide range of differential expression analysis scenarios encountered in single-cell RNA-seq scenarios and integrates into scanpy_ workflows. Import diffxpy as `import diffxpy.api as de` to access the following differential expression analysis-related tools: - 1. *differential expression analysis* in the module `de.test.*` - 2. *gene set enrichment analysis* based on differential expression calls in the module `de.enrich.*` +1. _differential expression analysis_ in the module `de.test.*` +2. _gene set enrichment analysis_ based on differential expression calls in the module `de.enrich.*` Refer to the documentation_ and the tutorials_ for details of these modules. From 6c6d1f0c8aeddd9b4bfb00e3a1c0abb5040fa82b Mon Sep 17 00:00:00 2001 From: "david.seb.fischer" Date: Wed, 14 Aug 2019 15:38:49 +0200 Subject: [PATCH 4/4] fixed heading and bold text in rst --- README.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index befc50b..f9df147 100644 --- a/README.rst +++ b/README.rst @@ -6,14 +6,14 @@ :target: https://diffxpy.readthedocs.io Fast and scalable differential expression analysis on single-cell RNA-seq data -=== +============================================================================== diffxpy covers a wide range of differential expression analysis scenarios encountered in single-cell RNA-seq scenarios and integrates into scanpy_ workflows. Import diffxpy as `import diffxpy.api as de` to access the following differential expression analysis-related tools: -1. _differential expression analysis_ in the module `de.test.*` -2. _gene set enrichment analysis_ based on differential expression calls in the module `de.enrich.*` +1. **differential expression analysis** in the module `de.test.*` +2. **gene set enrichment analysis** based on differential expression calls in the module `de.enrich.*` Refer to the documentation_ and the tutorials_ for details of these modules.