README.md

In biomics-pasteur-fr/RNADiff: R Tools for RNA-Seq Projects at Institut Pasteur (Biomics Platform)

Warning

This software is a R package originally developed within the Biomics Platform - Institut Pasteur to perform differential analysis of RNA-Seq data.

This repository is a fork of https://gitlab.pasteur.fr/hvaret/PF2tools software developped and maintained by Hugo Varet. This fork was made in Oct 2019 and is now maintained by the drylab group group of the Biomics Platform.

The development of PF2tools was originally developed within the Biomics Platform and for the Biomics Platform. The original code is now hosted in a different repository. Yet we wanted to keep this repository alive. Indeed, it is part of the software used for production within the Biomics Platform. This is a fork of version 1.6.3, which we tagged as 1.7.0. The main differences so far: - renaming the original repository into RNADiff - simplification of the reports - provide a reproducible container - add test files

How to install RNADiff ?

Manual

The installation requires several packages: DESeq2, edgeR, genefilter, xtable and knitr (all available online, see the dedicated webpages). As a DESeq2 or edgeR update might make the workflow unusable due to modifications on the statistical models, care is recommended when updating these packages.

To install the RNADiff package from GitHub, open a R session and: - install devtools with install.packages("devtools") (if not installed yet) - 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("biomics-pasteur-fr/RNADiff", build_vignettes=TRUE).

Note: Ubuntu users may have to install some libraries (libxml2-dev, libcurl4-openssl-dev and libssl-dev) to be able to install DESeq2 and devtools.

Please read the NEWS file to see the latest improvements!

Singularity

You may use damona (python package available on pypi):

damona install rnadiff:1.7.1

Note: you will need Singularity to be insalled on your system of course.

How to use RNADiff ?

Two vignettes are available within the package and provide extensive information. The user can access them via the vignettes directory on GitHub or running vignette("modeDemploiAnaDiff", package="RNADiff") in R.

biomics-pasteur-fr/RNADiff documentation built on Aug. 27, 2020, 12:44 a.m.