NxtIRFdata

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see NxtIRFdata.

Data for NxtIRF

Bioconductor version: 3.14

NxtIRFdata is a companion package for NxtIRF, which is an IRFinder- based R package for Intron Retention and Alternative Splicing quantitation for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains a synthetic genome reference and example BAM files used to test NxtIRF. BAM files are based on 6 samples from the Leucegene dataset provided by NCBI Gene Expression Omnibus under accession number GSE67039.

Author: Alex Chit Hei Wong [aut, cre, cph], Ulf Schmitz [ctb]

Maintainer: Alex Chit Hei Wong <a.wong at centenary.org.au>

Citation (from within R, enter citation("NxtIRFdata")):

Installation

To install this package, start R (version "4.1") and enter:


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

BiocManager::install("NxtIRFdata")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("NxtIRFdata")

NxtIRFdata: a data package for NxtIRF	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, ExpressionData, Genome, PackageTypeData, RNASeqData
Version	1.0.0
License	MIT + file LICENSE
Depends
Imports	ExperimentHub, BiocFileCache, rtracklayer, R.utils
System Requirements
URL	https://github.com/alexchwong/NxtIRFdata
Bug Reports	https://support.bioconductor.org/

Suggests	testthat (>= 3.0.0), knitr, rmarkdown
Linking To
Enhances
Depends On Me	NxtIRFcore
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	NxtIRFdata_1.0.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/NxtIRFdata
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NxtIRFdata
Package Short Url	https://bioconductor.org/packages/NxtIRFdata/
Package Downloads Report	Download Stats