JunctionSeq
This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see JunctionSeq.
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
Bioconductor version: 3.11
A Utility for Detection and Visualization of Differential Exon or Splice-Junction Usage in RNA-Seq data.
Author: Stephen Hartley [aut, cre] (PhD), Simon Anders [cph], Alejandro Reyes [cph]
Maintainer: Stephen Hartley <JunctionSeq-contact at list.nih.gov>
citation("JunctionSeq")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("JunctionSeq")
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("JunctionSeq")| JunctionSeq Vignette | |
| Reference Manual | |
| NEWS | Text |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | file LICENSE |
| Depends | R (>= 3.2.2), methods, SummarizedExperiment(>= 0.2.0), Rcpp (>= 0.11.0), RcppArmadillo (>= 0.3.4.4) |
| Imports | DESeq2(>= 1.10.0), statmod, Hmisc, plotrix, stringr, Biobase(>= 2.30.0), locfit, BiocGenerics(>= 0.7.5), BiocParallel, genefilter, geneplotter, S4Vectors, IRanges, GenomicRanges |
| System Requirements | |
| URL | http://hartleys.github.io/JunctionSeq/index.html |
| Bug Reports | https://github.com/hartleys/JunctionSeq/issues |
See More
| Suggests | MASS, knitr, JctSeqData, BiocStyle |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | Cairo, pryr |
| Depends On Me | |
| Imports Me | PathwaySplice |
| Suggests Me | JctSeqData, snapcount |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | JunctionSeq_1.17.0.tar.gz |
| Windows Binary | JunctionSeq_1.17.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | |
| Source Repository | git clone https://git.bioconductor.org/packages/JunctionSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/JunctionSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/JunctionSeq/ |
| Package Short Url | https://bioconductor.org/packages/JunctionSeq/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |