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("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 | ||
| 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 |