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Splice event prediction and quantification from RNA-seq data

Bioconductor version: Release (3.19)

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.

Author: Leonard Goldstein [cre, aut]

Maintainer: Leonard Goldstein <ldgoldstein at>

Citation (from within R, enter citation("SGSeq")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

SGSeq HTML R Script
Reference Manual PDF


biocViews AlternativeSplicing, ImmunoOncology, RNASeq, Software, Transcription
Version 1.38.0
In Bioconductor since BioC 3.0 (R-3.1) (10 years)
License Artistic-2.0
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), grDevices, graphics, igraph, parallel, rtracklayer(>= 1.39.7), stats
System Requirements
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Suggests BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown
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Depends On Me EventPointer
Imports Me Rhisat2
Suggests Me FRASER
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SGSeq_1.38.0.tar.gz
Windows Binary
macOS Binary (x86_64) SGSeq_1.38.0.tgz
macOS Binary (arm64) SGSeq_1.38.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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