mosdef
MOSt frequently used and useful Differential Expression Functions
Bioconductor version: 3.23 · Package version: 1.8.0
This package provides functionality to run a number of tasks in the differential expression analysis workflow. This encompasses the most widely used steps, from running various enrichment analysis tools with a unified interface to creating plots and beautifying table components linking to external websites and databases. This streamlines the generation of comprehensive analysis reports.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("mosdef") Details
| Maintainer | Federico Marini <marinif@uni-mainz.de> |
| Author | Leon Dammer [aut] (ORCID: <https://orcid.org/0009-0008-4132-7639>), Federico Marini [aut, cre] (ORCID: <https://orcid.org/0000-0003-3252-7758>) |
| License | MIT + file LICENSE |
| URL | https://github.com/imbeimainz/mosdef |
| Bug Reports | https://github.com/imbeimainz/mosdef/issues |
| Downloads rank | 415 |
| Source branch | RELEASE_3_23 |
| biocViews | DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, ReportWriting, Software, Transcription, Transcriptomics, Visualization |
Documentation
Download
Dependencies
Depends: R (>= 4.4.0)
Imports: DT, ggplot2, ggforce, ggrepel, graphics, grDevices, htmltools, methods, AnnotationDbi, topGO, GO.db, clusterProfiler, goseq, utils, RColorBrewer, rlang, DESeq2, scales, SummarizedExperiment, S4Vectors, stats
Suggests: knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene, BiocStyle
Reverse dependencies
Imports Me (3): GeneTonic, ideal, pcaExplorer
Suggests Me (2): DeeDeeExperiment, GeDi