DOI: 10.18129/B9.bioc.NxtIRFcore    

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

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

Bioconductor version: Development (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>

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HTML R Script NxtIRFcore: Differential Alternative Splicing and Intron Retention analysis
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biocViews AlternativeSplicing, Coverage, DifferentialSplicing, RNASeq, Software, Transcriptomics
Version 1.5.0
In Bioconductor since BioC 3.14 (R-4.1) (1 year)
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
URL https://github.com/alexchwong/NxtIRFcore
BugReports https://support.bioconductor.org/
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Source Package NxtIRFcore_1.5.0.tar.gz
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