Statistical Analysis of RNA-Seq Tools
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inst statColumnDESeq2 Sep 25, 2018
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DESCRIPTION 1.6.6 Oct 4, 2018
NAMESPACE 1.5.0 Jun 1, 2017
NEWS 1.6.6 Oct 4, 2018
README.md 1.6.0 Dec 11, 2017
template_script_DESeq2.r
template_script_DESeq2_CL.r 1.6.6 Oct 4, 2018
template_script_edgeR.r 1.6.6 Oct 4, 2018
template_script_edgeR_CL.r 1.6.6 Oct 4, 2018

README.md

SARTools

SARTools is a R package dedicated to the differential analysis of RNA-seq data. It 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.

SARTools is distributed with two R script templates (template_script_DESeq2.r and template_script_edgeR.r) which use functions of the package. For a more fluid analysis and to avoid possible bugs when creating the final HTML report, the user is encouraged to use them rather than writing a new script. Two other scripts are available (template_script_DESeq2_CL.r and template_script_edgeR_CL.r) to run SARTools in a shell with the Rscript command. In that case, the optparse R package must be available to interpret the command line parameters.

How to install SARTools?

Within R

In addition to the SARTools package itself, the workflow requires the installation of several packages: DESeq2, edgeR, genefilter, xtable and knitr (all available online, see the dedicated webpages). SARTools needs R version 3.3.0 or higher, DESeq2 1.12.0 or higher and edgeR 3.12.0 or higher: old versions of DESeq2 or edgeR may be incompatible with SARTools.

To install the SARTools package from GitHub, open a R session and:

  • install DESeq2, edgeR and genefilter with source("http://bioconductor.org/biocLite.R") and biocLite(c("DESeq2", "edgeR", "genefilter")) (if not installed yet)

  • install devtools with install.packages("devtools") (if not installed yet)

  • Notes:

    • Ubuntu users may have to install some libraries (libxml2-dev, libcurl4-openssl-dev and libssl-dev) to be able to install DESeq2 and devtools
    • Some users may have to install the pandoc and pandoc-citeproc libraries to be able to generate the final HTML reports
  • for Windows users only, install Rtools or check that it is already installed (needed to build the package)

  • load the devtools R package with library(devtools)

  • run install_github("PF2-pasteur-fr/SARTools", build_vignettes=TRUE)

Using Conda

install with bioconda

  1. Install miniconda2
  2. Install the SARTools R library and its dependencies using conda conda install r-sartools

Note: if you want to set a dedicated conda environment for SARTools, use conda create -n sartools r-sartools and follow the instructions to activate it.

How to use SARTools?

A HTML vignette is available within the vignettes folder on GitHub and provides extensive information on the use of SARTools. The user can also open it with vignette("SARTools") if it has been generated during the installation of the package.

Be careful to use the R script associated with the version of SARTools installed on your system.

Please read the NEWS file to see the latest improvements!

About SARTools

The SARTools package has been developped at PF2 - Institut Pasteur by M.-A. Dillies and H. Varet (hugo.varet@pasteur.fr). 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.