Package: SGSeq
Type: Package
Title: Splice event prediction and quantification from RNA-seq data
Version: 1.43.1
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
git_url: https://git.bioconductor.org/packages/SGSeq
git_branch: devel
git_last_commit: de154f1
git_last_commit_date: 2025-07-22
Repository: Bioconductor 3.22
Date/Publication: 2025-07-23
NeedsCompilation: no
Packaged: 2025-07-24 02:14:46 UTC; biocbuild
Author: Leonard Goldstein [cre, aut]
Maintainer: Leonard Goldstein <ldgoldstein@gmail.com>
Built: R 4.5.1; ; 2025-07-24 14:11:32 UTC; windows
