NxtIRFcore

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

This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see NxtIRFcore.

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


Bioconductor version: 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) (2.5 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
System Requirements C++11
URL https://github.com/alexchwong/NxtIRFcore
Bug Reports https://support.bioconductor.org/
See More
Suggests knitr, rmarkdown, pheatmap, shiny, openssl, crayon, egg, DESeq2, limma, DoubleExpSeq, Rsubread, testthat (>= 3.0.0)
Linking To Rcpp, zlibbioc, RcppProgress
Enhances
Depends On Me
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 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
Old Source Packages for BioC 3.17 Source Archive