DRIMSeq
This is the released version of DRIMSeq; for the devel version, see DRIMSeq.
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Bioconductor version: Release (3.23)
The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the 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.uzh at gmail.com>
citation("DRIMSeq")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DRIMSeq")
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("DRIMSeq")| Differential transcript usage and transcript usage QTL analyses in RNA-seq with the DRIMSeq package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, ImmunoOncology, MultipleComparison, RNASeq, SNP, Sequencing, Software, WorkflowStep |
| Version | 1.40.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 3.4.0) |
| Imports | utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2 |
| System Requirements | |
| URL |
See More
| Suggests | PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | rnaseqDTU |
| Imports Me | BANDITS |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DRIMSeq_1.40.0.tar.gz |
| Windows Binary (x86_64) | DRIMSeq_1.40.0.zip |
| macOS Binary (big-sur-x86_64) | DRIMSeq_1.40.0.tgz |
| macOS Binary (sonoma-arm64) | DRIMSeq_1.40.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DRIMSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DRIMSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/DRIMSeq/ |
| Package Short Url | https://bioconductor.org/packages/DRIMSeq/ |
| Package Downloads Report | Download Stats |