Package: SGSeq
Type: Package
Title: Splice event prediction and quantification from RNA-seq data
Version: 1.44.0
Authors@R: person("Leonard", "Goldstein", email = "ldgoldstein@gmail.com", role = c("cre", "aut"))
Description: SGSeq is a software package for analyzing splice events
        from RNA-seq data. Input data are RNA-seq reads mapped to a
        reference genome in BAM format. Genes are represented as a
        splice graph, which can be obtained from existing annotation or
        predicted from the mapped sequence reads. Splice events are
        identified from the graph and are quantified locally using
        structurally compatible reads at the start or end of each
        splice variant. The software includes functions for splice
        event prediction, quantification, visualization and
        interpretation.
License: Artistic-2.0
LazyData: yes
Depends: R (>= 4.0), IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10),
        Rsamtools (>= 1.31.2), SummarizedExperiment, methods
Imports: AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>=
        2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>=
        1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19), Seqinfo,
        grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7),
        stats
Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
        TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown
VignetteBuilder: knitr
biocViews: AlternativeSplicing, ImmunoOncology, RNASeq, Transcription
RoxygenNote: 6.0.1
Config/pak/sysreqs: libglpk-dev make libbz2-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:22:27 UTC
RemoteUrl: https://github.com/bioc/SGSeq
RemoteRef: RELEASE_3_22
RemoteSha: 2a90d1b16e57653bc19d32eedf3c9e0cec1b11a7
NeedsCompilation: no
Packaged: 2026-01-24 20:52:44 UTC; root
Author: Leonard Goldstein [cre, aut]
Maintainer: Leonard Goldstein <ldgoldstein@gmail.com>
Built: R 4.5.2; ; 2026-01-24 21:17:42 UTC; unix
