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NxtIRFdata

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

Data for NxtIRF


Bioconductor version: Development (3.20)

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 <a.wong at centenary.org.au>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
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

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, Genome, PackageTypeData, RNASeqData
Version 1.11.0
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/
See More
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_1.11.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (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