From 3ba21a00e7f59cf86be16f462a75262a53a9ffb0 Mon Sep 17 00:00:00 2001 From: Aurore Comte <aurore.f.comte@gmail.com> Date: Fri, 23 Sep 2022 16:33:03 +0200 Subject: [PATCH] Update and rename README.rst to README.md --- README.md | 48 ++++++++++++++++++++++++++++++++++++++++++ README.rst | 61 ------------------------------------------------------ 2 files changed, 48 insertions(+), 61 deletions(-) create mode 100644 README.md delete mode 100644 README.rst diff --git a/README.md b/README.md new file mode 100644 index 0000000..00b999b --- /dev/null +++ b/README.md @@ -0,0 +1,48 @@ +# RNAja + +[](https://www.python.org/downloads) +[](https://snakemake.readthedocs.io) +[](https://sylabs.io/docs/) + +About RNAja +=============== + +RNAja is a pipeline written in snakemake. +It's aim is to analyse RNAseq data, perform differential expression analysis on it and output a report in Rmarkdown. +The output are compatible with the database diffexDB https://bioinfo-web.mpl.ird.fr/cgi-bin2/microarray/public/diffexdb.cgi. + + +**Homepage:** + +TODO + + +## Authors + +- Aurore Comte (IRD) + +Some parts of RNAja code and documentation were inspired or came from the pipelines below. + +- Culebront (Julie Orjuela *et al.*) https://github.com/SouthGreenPlatform/culebrONT + +- sRNAmake (Sebastien Cunnac *et al.*) https://github.com/Aucomte/sRNAmake + +- BulkRNA (Camille Cohen) https://github.com/CamilleCohen/ProjetTuteur-_BulkRNA + +Thanks and aknowledgements +========================== + +Thanks to Ndomassi Tando (i-Trop IRD) by administration support. + +The authors acknowledge the IRD i-Trop HPC <https://bioinfo.ird.fr/> (South Green Platform <http://www.southgreen.fr>) at IRD +Montpellier for providing HPC resources that have contributed to this work. + +Thanks to Alexis Dereeper for his help and the developpement of diffexDB <https://bioinfo-web.mpl.ird.fr/cgi-bin2/microarray/public/diffexdb.cgi>. + +License +======= + +Licencied under CeCill-C http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html> and GPLv3. + +Intellectual property belongs to IRD and authors. + diff --git a/README.rst b/README.rst deleted file mode 100644 index 372e2e0..0000000 --- a/README.rst +++ /dev/null @@ -1,61 +0,0 @@ -# RNAja - - -|PythonVersions| |SnakemakeVersions| |Singularity| - -.. contents:: Table of Contents - :depth: 2 - -About RNAja -=============== - -RNAja is a pipeline written in snakemake. -It's aim is to analyse RNAseq data, perform differential expression analysis on it and output a report in Rmarkdown. -The output are compatible with the database `diffexDB <https://bioinfo-web.mpl.ird.fr/cgi-bin2/microarray/public/diffexdb.cgi>`_. - -|readthedocs| - -**Homepage:** - -TODO - - -Authors -_______ - -* Aurore Comte (IRD) - -Some parts of RNAja code and documentation were inspired or came from the pipelines below. - -- Culebront (Julie Orjuela *et al.*) https://github.com/SouthGreenPlatform/culebrONT - -- sRNAmake (Sebastien Cunnac *et al.*) https://github.com/Aucomte/sRNAmake - -- BulkRNA (Camille Cohen) https://github.com/CamilleCohen/ProjetTuteur-_BulkRNA - -Thanks and aknowledgements -========================== - -Thanks to Ndomassi Tando (i-Trop IRD) by administration support. - -The authors acknowledge the `IRD i-Trop HPC <https://bioinfo.ird.fr/>`_ (`South Green Platform <http://www.southgreen.fr>`_) at IRD -Montpellier for providing HPC resources that have contributed to this work. - -Thanks to Alexis Dereeper for his help and the developpement of `diffexDB <https://bioinfo-web.mpl.ird.fr/cgi-bin2/microarray/public/diffexdb.cgi>`_. - -License -======= - -Licencied under `CeCill-C <http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html>`_ and GPLv3. - -Intellectual property belongs to IRD and authors. - -.. |PythonVersions| image:: https://img.shields.io/badge/python-3.7%2B-blue - :target: https://www.python.org/downloads -.. |SnakemakeVersions| image:: https://img.shields.io/badge/snakemake-≥5.10.0-brightgreen.svg?style=flat - :target: https://snakemake.readthedocs.io -.. |Singularity| image:: https://img.shields.io/badge/singularity-≥3.3.0-7E4C74.svg - :target: https://sylabs.io/docs/ -.. |readthedocs| image:: https://pbs.twimg.com/media/E5oBxcRXoAEBSp1.png - :target: https://culebront-pipeline.readthedocs.io/en/latest/ - :width: 400px -- GitLab