NxtIRFcore

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine

Bioconductor version: Release (3.17)

Interactively analyses Intron Retention and Alternative Splicing Events (ASE) in RNA-seq data. NxtIRF quantifies ASE events in BAM files aligned to the genome using a splice-aware aligner such as STAR. The core quantitation algorithm relies on the IRFinder/C++ engine ported via Rcpp for multi-platform compatibility. In addition, NxtIRF provides convenient pipelines for downstream analysis and publication-ready visualisation tools. Note that NxtIRFcore is now replaced by SpliceWiz in Bioconductor 3.16 onwards.

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

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

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

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("NxtIRFcore")

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("NxtIRFcore")

NxtIRFcore: Differential Alternative Splicing and Intron Retention analysis	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Details

biocViews	AlternativeSplicing, Coverage, DifferentialSplicing, RNASeq, Software, Transcriptomics
Version	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	MIT + file LICENSE
Depends	R (>= 3.5.0), NxtIRFdata
Imports	methods, stats, utils, tools, parallel, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, IRanges, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors
Linking To	Rcpp, zlibbioc, RcppProgress
Suggests	knitr, rmarkdown, pheatmap, shiny, openssl, crayon, egg, DESeq2, limma, DoubleExpSeq, Rsubread, testthat (>= 3.0.0)
System Requirements	C++11
Enhances
URL	https://github.com/alexchwong/NxtIRFcore
Bug Reports	https://support.bioconductor.org/

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Package Archives

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

Source Package	NxtIRFcore_1.6.0.tar.gz
Windows Binary	NxtIRFcore_1.6.0.zip
macOS Binary (x86_64)	NxtIRFcore_1.6.0.tgz
macOS Binary (arm64)	NxtIRFcore_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/NxtIRFcore
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NxtIRFcore
Package Short Url	https://bioconductor.org/packages/NxtIRFcore/
Package Downloads Report	Download Stats