SGSeq
Splice event prediction and quantification from RNA-seq data
Bioconductor version: Release (3.20)
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 gmail.com>
citation("SGSeq")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SGSeq")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SGSeq")| SGSeq | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, ImmunoOncology, RNASeq, Software, Transcription |
| Version | 1.40.0 |
| 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 | |
| URL |
See More
| Suggests | BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | EventPointer |
| Imports Me | Rhisat2 |
| Suggests Me | FRASER |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SGSeq_1.40.0.tar.gz |
| Windows Binary (x86_64) | SGSeq_1.40.0.zip |
| macOS Binary (x86_64) | SGSeq_1.40.0.tgz |
| macOS Binary (arm64) | SGSeq_1.39.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SGSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SGSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/SGSeq/ |
| Package Short Url | https://bioconductor.org/packages/SGSeq/ |
| Package Downloads Report | Download Stats |