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 (3.21)
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:
Maintainer: Federico Marini <marinif at uni-mainz.de>
citation("mosdef")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, ReportWriting, Software, Transcription, Transcriptomics, Visualization |
| Version | 1.3.1 |
| 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 |
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_1.3.1.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/ |
| Package Downloads Report | Download Stats |