mosdef
This is thereleased version of mosdef; for the devel version, seemosdef.
MOSt frequently used and useful Differential Expression Functions
Bioconductor version: Release (3.22)
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: 0009-0008-4132-7639, Federico Marini [aut, cre] ORCID: 0000-0003-3252-7758
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")BiocManager::install("mosdef")For older versions of R, please refer to the appropriateBioconductor 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 | 1.6.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2 years) |
| License | MIT + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | mosdef_1.6.0.tar.gz |
| Windows Binary (x86_64) | mosdef_1.6.0.zip |
| macOS Binary (x86_64) | mosdef_1.6.0.tgz |
| macOS Binary (arm64) | mosdef_1.6.0.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 |