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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DRIMSeq")
In most cases, you don't need to download the package archive at all.
DRIMSeq
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This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see DRIMSeq.
Differential splicing and sQTL analyses with Dirichlet-multinomial model in RNA-Seq
Bioconductor version: 3.4
The package provides two frameworks. One for the differential splicing analysis between different conditions and one for the sQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts, exons or exonic bins) with Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.
Author: Malgorzata Nowicka [aut, cre]
Maintainer: Malgorzata Nowicka <gosia.nowicka at uzh.ch>
Citation (from within R,
enter citation("DRIMSeq")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DRIMSeq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DRIMSeq")
| R Script | Differential splicing and sQTL analyses in RNA-seq with 'DRIMSeq' package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, MultipleComparison, RNASeq, SNP, Sequencing, Software, WorkflowStep |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1 year) |
| License | GPL (>= 3) |
| Depends | R (>= 3.3.0) |
| Imports | GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, edgeR, utils, stats, grDevices, ggplot2, reshape2 |
| LinkingTo | |
| Suggests | PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DRIMSeq_1.2.0.tar.gz |
| Windows Binary | DRIMSeq_1.2.0.zip |
| Mac OS X 10.9 (Mavericks) | DRIMSeq_1.2.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DRIMSeq/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/DRIMSeq/ |
| Package Downloads Report | Download Stats |
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