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mosdef (development version)

mosdef

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

MOSt frequently used and useful Differential Expression Functions

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DOI: 10.18129/B9.bioc.mosdef

Bioconductor version: Development (3.23)

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] ORCID iD ORCID: 0009-0008-4132-7639 , Federico Marini [aut, cre] ORCID iD ORCID: 0000-0003-3252-7758

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

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

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, ReportWriting, Software, Transcription, Transcriptomics, Visualization

Version 1.7.0

In Bioconductor since BioC 3.19 (R-4.4) (1.5 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

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 DeeDeeExperiment, GeDi

Links To Me

Build Report Build Report

Package Archives

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

Source Package mosdef_1.7.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

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/

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