ngsRtools

A Suite of R Packages for NGS-based Epigenomic Data Analysis.

Description

A Collection of Statistical and Visualization Tools for Next-Generation Sequencing Data Analysis, with a focus on Epigenomics research.

It includes packages for the analysis of:

• RNA-seq (bulk transcriptomics) - RNAseqRtools
  
• scRNA-seq (single-cell transcriptomics) - scRNAseqRtools
  
• ChIP-seq (genome-wide Protein-DNA binding) - ChIPseqRtools
  
• BS-seq (genome-wide DNA methylation analysis) - BSseqRtools
  
• Sequence Data processing and analysis - sequenceAnalysisRtools
  

Prerequisites

The suite is based on a set of CRAN and R/Bioconductor packages. The complete list of required packages is reported here for each component of the suite:

• RNAseqRtools: edgeR, DESeq2, sva, cluster, gProfileR, clusterProfiler, dynamicTreeCut, ComplexHeatmap.
  
• scRNAseqRtools: scater, scran, monocle.
  
• ChIPseqRtools: GenomicRanges.
  
• BSseqRtools: methylKit.
  
• sequenceAnalysisRtools: Biostrings.
  
• utilsRtools: ggplot2, reshape2, plyr.
  

The installation script will automatically take care of dependencies (see Installation section).

Installation

Clone the repository on your machine:

git clone https://github.com/andrealauria104/ngsRtools.git

To install the complete suite of packages:

cd ngsRtools
./install.sh

This will install packages and dependencies. It will also test executability of programs in the scripts/ folder.
Alternatively, yuo can install individual packages, for example typing from your R session:

devtools::install_github("https://github.com/andrealauria104/ngsRtools", subdir="packages/RNAseqRtools")

Or from the location of you cloned repository:

# from command line
R CMD INSTALL RNAseqRtools

# from R
devtools::install("RNAseqRtools")

Warning: all packages depend from the utilsRtools package. If you choose to install individual packages, install it as you first.
To uninstall the complete suite:

cd ngsRtools
./uninstall.sh

Using Conda

Clone the repository on your machine:

git clone https://github.com/andrealauria104/ngsRtools.git

Create conda environment from .yml file with all R dependencies:

cd ngsRtools
conda env create -f data/environment.yml -n r-environment

Activate r-environment and install the complete suite of packages:

conda activate r-environment
cd ngsRtools
./install.sh

The suite will now be available activating the conda environment.

Docker

The suite can be used in a Docker container with all packages and scripts. Pull the image:

docker pull anlauria/ngsrtools

To run interactive bash in current directory

docker run --rm -it -u `id -u`:`id -g` -v $(pwd):/tmp/ anlauria/ngsrtools:0.0.1 bash

To run interactive R console in current directory

docker run --rm -it -u `id -u`:`id -g` -v $(pwd):/tmp/ anlauria/ngsrtools:0.0.1 R

To run RStudio server in current directory - localhost:8787, username=rstudio

docker run --rm -v $(pwd):/home/rstudio -e PASSWORD="ngsrtools" -p 8787:8787 anlauria/ngsrtools:0.0.1