mosdef

This is the development version of mosdef; for the stable release version, see mosdef.

MOSt frequently used and useful Differential Expression Functions


Bioconductor version: Development (3.20)

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.

Author: Leon Dammer [aut] , Federico Marini [aut, cre]

Maintainer: Federico Marini <marinif at uni-mainz.de>

Citation (from within R, enter citation("mosdef")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("mosdef")

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("mosdef")
The mosdef User's Guide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, ReportWriting, Software, Transcription, Transcriptomics, Visualization
Version 1.1.3
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
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
System Requirements
URL https://github.com/imbeimainz/mosdef
Bug Reports https://github.com/imbeimainz/mosdef/issues
See More
Suggests knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me GeneTonic, ideal, pcaExplorer
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package mosdef_1.1.3.tar.gz
Windows Binary mosdef_1.1.3.zip (64-bit only)
macOS Binary (x86_64) mosdef_1.1.3.tgz
macOS Binary (arm64) mosdef_1.1.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/mosdef
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/mosdef
Bioc Package Browser https://code.bioconductor.org/browse/mosdef/
Package Short Url https://bioconductor.org/packages/mosdef/
Package Downloads Report Download Stats