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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 1.1.0
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, 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
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Build Report Build Report

Package Archives

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

Source Package mosdef_1.1.0.tar.gz
Windows Binary mosdef_1.1.0.zip (64-bit only)
macOS Binary (x86_64) mosdef_1.1.0.tgz
macOS Binary (arm64) mosdef_1.1.0.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