# 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install.packages("BiocManager") BiocManager::install(version = "devel") BiocManager::valid() # checks for out of date packages BiocManager::install("NxtIRFcore") ``` * Development version from Github (NxtIRFcore and its dependency NxtIRFdata): ``` library("devtools")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quietly=TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.14") BiocManager::valid() # checks for out of date packages BiocManager::install("NxtIRFcore") ``` ### On R == 4.0.x * As NxtIRFcore's vignette relies on a demo dataset that is deposited in AnnotationHub for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