mosdef

MOSt frequently used and useful Differential Expression Functions

Bioconductor version: Release (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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, ReportWriting, Software, Transcription, Transcriptomics, Visualization
Version	1.2.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
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

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_1.2.0.tar.gz
Windows Binary (x86_64)	mosdef_1.2.0.zip (64-bit only)
macOS Binary (x86_64)	mosdef_1.2.0.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