Mercurial > repos > lgueguen > sartools
comparison README.md @ 4:05c9b1a7f44e draft default tip
Uploaded new release 1.7.3
| author | lgueguen |
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| date | Thu, 07 Jan 2021 11:12:01 +0000 |
| parents | de6d0b7c17af |
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| 1 -------------------------------------------------------------------------------------- | |
| 2 SARTools-Galaxy: a galaxy wrapper for SARTools (Statistical Analysis of RNA-Seq Tools) | |
| 3 -------------------------------------------------------------------------------------- | |
| 4 | |
| 5 [](https://travis-ci.org/PF2-pasteur-fr/SARTools-Galaxy) | |
| 6 | |
| 7 Description: | |
| 8 ------------ | |
| 9 SARTools is a R package dedicated to the differential analysis of RNA-seq data. | |
| 10 | |
| 11 SARTools provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis. Note that SARTools does not intend to replace DESeq2 or edgeR: it simply provides an environment to go with them. For more details about the methodology behind DESeq2 or edgeR, the user should read their documentations and papers. | |
| 12 | |
| 13 Requirements: | |
| 14 ------------- | |
| 15 These Galaxy tools need: | |
| 16 - R and the following R packages: SARTools, DESeq2, edgeR, genefilter, xtable and knitr. | |
| 17 - Rscript and optparse package | |
| 18 | |
| 19 SARTools can be downloaded on github (https://github.com/PF2-pasteur-fr/SARTools). More information about installation can be found at this url. | |
| 20 | |
| 21 Requirements using Conda: | |
| 22 ------------------------- | |
| 23 [](http://bioconda.github.io/recipes/r-sartools/README.html) | |
| 24 | |
| 25 [Conda](http://conda.pydata.org/) is package manager that among many other things can be used to manage Python packages. | |
| 26 | |
| 27 | |
| 28 ``` | |
| 29 #To install miniconda2 | |
| 30 #http://conda.pydata.org/miniconda.html | |
| 31 #To install the SARTools R library using conda: | |
| 32 conda install r-sartools | |
| 33 #To set an environment: | |
| 34 conda create -n r-sartools r-sartools` | |
| 35 #To activate the environment: | |
| 36 . activate r-sartools | |
| 37 ``` | |
| 38 | |
| 39 | |
| 40 Test: | |
| 41 ----- | |
| 42 | |
| 43 `planemo test` using conda: passed | |
| 44 | |
| 45 | |
| 46 References: | |
| 47 ----------- | |
| 48 The SARTools package has been developped at PF2 - Institut Pasteur by M.-A. Dillies and H. Varet (hugo.varet@pasteur.fr). | |
| 49 Thanks to cite H. Varet, L. Brillet-Guéguen, J.-Y. Coppee and M.-A. Dillies, SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data, PLoS One, 2016, doi: http://dx.doi.org/10.1371/journal.pone.0157022 when using this tool for any analysis published. | |
| 50 | |
| 51 The Galaxy wrapper and scripts have been developped by Loraine Brillet-Guéguen, Institut Français de Bioinformatique | |
| 52 |