metaseqR2

An R package for the analysis, meta-analysis and result reporting of RNA-Seq gene expression data - Next Generation!

Citation

metaseqR2 along with further research regarding the abilities of the PANDORA algorithm was published in Briefings in Bioinformatics. If you use metaseqR2 in your research, please cite:

Dionysios Fanidis, Panagiotis Moulos: Integrative, normalization-insusceptible statistical analysis of RNA-Seq data, with improved differential expression and unbiased downstream functional analysis, Briefings in Bioinformatics, 2020, bbaa156, DOI: 10.1093/bib/bbaa156

Installation from Bioconductor

if (!requireNamespace("BiocManager",quietly=TRUE))
    install.packages("BiocManager")

library(BiocManager)

BiocManager::install("metaseqR2")

# or for development version to be installed
# BiocManager::install("metaseqR2",version="devel")

Installation from GitHub

Use with caution as the latest version may be unstable, although typical Bioconductor checks are executed before each push.

if (!requireNamespace("devtools",quietly=TRUE))
    install.packages("devtools")

library(devtools)
install_github("pmoulos/metaseqR2")

Installation from source

The same things apply regarding stability.

git clone https://github.com/pmoulos/metaseqR2.git
mkdir metaseqR2-build
rsync -avr --exclude=README.md --exclude=.git --exclude=.gitignore  \
    ./metaseqR2-local/ ./metaseqR2-build/metaseqR2
cd ./metaseqR2-build
R CMD build ./metaseqR2

This will take some time to build the vignettes. If you do not need them:

R CMD build --no-build-vignettes ./metaseqR2

And then install

R CMD INSTALL ./metaseqR2_x.y.z.tar.gz

Please report any issues here.

metaseqR2 annotation database

If you do not wish to build annotation databases on your own using the buildAnnotationDatabase function, you can find complete pre-built annotation SQLite databases here. New versions will be constructed from time to time, most probably whenever a new Ensembl release comes live.

The prebuilt annotations contain:

• Annotations for all supported organsisms for all types of metaseqR2 analyses.
• For every supported organism:
  • For the latest version of each genome, the latest two Ensembl required annotations.
  • For all other versions of each genome, the latest Ensembl required annotations supporting that particular version.
  • UCSC and RefSeq annotations as fetched in the day of the build (denoted by the folder name in the above link).

The SQLite database must be placed in system.file(package="metaseqR2") and named annotation.sqlite, that is file.path(system.file(package="metaseqR2"),"annotation.sqlite"). Otherwise you will have to provide your desired location in each metaseqr2 call. Alternatively, on-the-fly download is still supported but is inneficient.

List of required packages

metaseqR2 would benefit from the existence of all the following packages:

• ABSSeq
• Biobase
• BiocGenerics
• BiocManager
• BiocParallel
• BiocStyle
• biomaRt
• Biostrings
• BSgenome
• corrplot
• DESeq2
• DSS
• DT
• EDASeq
• edgeR
• harmonicmeanp
• genefilter
• GenomeInfoDb
• GenomicAlignments
• GenomicFeatures
• GenomicRanges
• gplots
• graphics
• grDevices
• heatmaply
• htmltools
• httr
• IRanges
• jsonlite
• knitr
• limma
• log4r
• magrittr
• Matrix
• methods
• NBPSeq
• pander
• parallel
• qvalue
• rmarkdown
• rmdformats
• RMySQL
• Rsamtools
• RSQLite
• rtracklayer
• RUnit
• S4Vectors
• splines
• stats
• stringr
• SummarizedExperiment
• survcomp
• TCC
• utils
• VennDiagram
• vsn
• zoo

A recent version of Pandoc is also required, ideally above 2.0.