Package: NxtIRFcore
Title: Core Engine for NxtIRF: a User-Friendly Intron Retention and
        Alternative Splicing Analysis using the IRFinder Engine
Version: 1.4.0
Date: 2022-10-25
Authors@R: c(person("Alex Chit Hei", "Wong", email="a.wong@centenary.org.au", 
		role=c("aut", "cre", "cph")),
	person("William", "Ritchie", role=c("cph")),
	person("Ulf", "Schmitz", role=c("ctb")))
Description: 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.
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)
VignetteBuilder: knitr
biocViews: Software, Transcriptomics, RNASeq, AlternativeSplicing,
        Coverage, DifferentialSplicing
SystemRequirements: C++11
Collate: AllImports.R RcppExports.R AllClasses.R AllGenerics.R
        NxtFilter-methods.R NxtSE-methods.R globals.R ggplot_themes.R
        example_data.R wrappers.R make_plot_data.R Coverage.R utils.R
        File_finders.R BuildRef.R STAR_utils.R Mappability.R IRFinder.R
        CollateData.R MakeSE.R Filters.R ASE-methods.R
        NxtIRFcore-package.R
Encoding: UTF-8
RoxygenNote: 7.1.2
URL: https://github.com/alexchwong/NxtIRFcore
BugReports: https://support.bioconductor.org/
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/NxtIRFcore
git_branch: RELEASE_3_16
git_last_commit: c38d908
git_last_commit_date: 2022-11-01
Date/Publication: 2022-11-01
NeedsCompilation: yes
Packaged: 2022-11-02 01:55:02 UTC; biocbuild
Author: Alex Chit Hei Wong [aut, cre, cph],
  William Ritchie [cph],
  Ulf Schmitz [ctb]
Maintainer: Alex Chit Hei Wong <a.wong@centenary.org.au>
Built: R 4.2.1; x86_64-w64-mingw32; 2022-11-02 14:01:40 UTC; windows
ExperimentalWindowsRuntime: ucrt
Archs: x64
