DRIMSeq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Bioconductor version: 3.23 · Package version: 1.40.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DRIMSeq")Details
| Maintainer | Malgorzata Nowicka <gosia.nowicka.uzh@gmail.com> |
| Author | Malgorzata Nowicka [aut, cre] |
| License | GPL (>= 3) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, ImmunoOncology, MultipleComparison, RNASeq, SNP, Sequencing, Software, WorkflowStep |
| Package Short Url | https://bioconductor.org/packages/DRIMSeq/ |
Citation
From within R, enter citation("DRIMSeq"):
Malgorzata Nowicka. DRIMSeq: Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq. doi:10.18129/B9.bioc.DRIMSeq, R package version 1.40.0, https://bioconductor.org/packages/DRIMSeq.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the 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 (arm64) | DRIMSeq_1.40.0.tgz |
| macOS binary (x86_64) | DRIMSeq_1.40.0.tgz |
Dependencies
Depends: R (>= 3.4.0)
Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2
Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat