Package: SGSeq Type: Package Title: Splice event prediction and quantification from RNA-seq data Version: 1.46.0 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: Bioconductor 3.23 Date/Publication: 2026-04-28 12:40:03 UTC RemoteUrl: https://github.com/bioc/SGSeq RemoteRef: RELEASE_3_23 RemoteSha: e9ed5aba2fec823647a15626791c5df53349a634 NeedsCompilation: no Packaged: 2026-10-12 09:33:14 UTC; root Author: Leonard Goldstein [cre, aut] Maintainer: Leonard Goldstein