NxtIRFcore

DOI: 10.18129/B9.bioc.NxtIRFcore    

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

Bioconductor version: Release (3.14)

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.

Author: Alex Chit Hei Wong [aut, cre, cph], William Ritchie [aut, 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 "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews AlternativeSplicing, Coverage, DifferentialSplicing, RNASeq, Software, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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
LinkingTo Rcpp, zlibbioc, RcppProgress
Suggests knitr, rmarkdown, pheatmap, shiny, openssl, crayon, egg, DESeq2, limma, DoubleExpSeq, Rsubread, testthat (>= 3.0.0)
SystemRequirements C++11
Enhances
URL https://github.com/alexchwong/NxtIRFcore
BugReports https://support.bioconductor.org/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package NxtIRFcore_1.0.0.tar.gz
Windows Binary NxtIRFcore_1.0.0.zip
macOS 10.13 (High Sierra) NxtIRFcore_1.0.0.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 3.14 Source Archive

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