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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

MaintainerFederico Marini <marinif@uni-mainz.de>
AuthorLeon Dammer [aut] (ORCID: <https://orcid.org/0009-0008-4132-7639>), Federico Marini [aut, cre] (ORCID: <https://orcid.org/0000-0003-3252-7758>)
LicenseMIT + file LICENSE
URLhttps://github.com/imbeimainz/mosdef
Bug Reportshttps://github.com/imbeimainz/mosdef/issues
Downloads rank415
Source branchRELEASE_3_23
biocViewsDifferentialExpression, 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