NxtIRFdata

This is the development version of NxtIRFdata; for the stable release version, see NxtIRFdata.

Data for NxtIRF

Bioconductor version: Development (3.24)

NxtIRFdata is a companion package for SpliceWiz, an interactive analysis and visualization tool for alternative splicing quantitation (including intron retention) 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 demonstrate SpliceWiz's functionality. 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 <alexchwong.github at gmail.com>

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

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	1.19.0
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	SpliceWiz
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_1.19.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
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