NxtIRFcore: Command line NxtIRF for Bioconductor

NxtIRF quantifies Intron Retention and Alternative Splicing from BAM files using the IRFinder engine. Features interactive visualisation including RNA-seq coverage plots normalised by condition at the splice junction level.

NxtIRF release version: http://www.bioconductor.org/packages/release/bioc/html/NxtIRFcore.html

NxtIRF devel version: http://www.bioconductor.org/packages/devel/bioc/html/NxtIRFcore.html

Installation

On devel R (>= 4.2.0)

• Requires Bioconductor devel version:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "devel")
BiocManager::valid()              # checks for out of date packages

BiocManager::install("NxtIRFcore")

• Development version from Github (NxtIRFcore and its dependency NxtIRFdata):

library("devtools")
install_github("alexchwong/NxtIRFdata")
install_github("alexchwong/NxtIRFcore", dependencies=TRUE, build_vignettes=TRUE)

On current version of R == 4.1.x

• Requires Bioconductor release version:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.14")
BiocManager::valid()              # checks for out of date packages

BiocManager::install("NxtIRFcore")

On R == 4.0.x

• As NxtIRFcore's vignette relies on a demo dataset that is deposited in AnnotationHub for Bioconductor 3.14, the vignette cannot be installed in R 4.0. The following should still work for Bioconductor 3.12 or 3.13. A warning that NxtIRF on old versions of Bioconductor have not been extensively tested, and unknown bugs may exist.

library("devtools")
install_github("alexchwong/NxtIRFdata")
install_github("alexchwong/NxtIRFcore", dependencies=TRUE, build_vignettes=FALSE)

Vignettes

• From within R, after installing NxtIRFcore:

browseVignettes("NxtIRFcore")

• You can also view the online version at Bioconductor here: http://www.bioconductor.org/packages/release/bioc/vignettes/NxtIRFcore/inst/doc/NxtIRF.html