Package: mosdef 1.9.0

Federico Marini

mosdef: MOSt frequently used and useful Differential Expression Functions

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.

Authors:Leon Dammer [aut], Federico Marini [aut, cre]

mosdef_1.9.0.tar.gz
mosdef_1.9.0.zip(r-4.7)mosdef_1.9.0.zip(r-4.6)mosdef_1.9.0.zip(r-4.5)
mosdef_1.9.0.tgz(r-4.6-any)mosdef_1.9.0.tgz(r-4.5-any)
mosdef_1.9.0.tar.gz(r-4.7-any)mosdef_1.9.0.tar.gz(r-4.6-any)
mosdef_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
mosdef/json (API)
NEWS

# Install 'mosdef' in R:
install.packages('mosdef', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/imbeimainz/mosdef/issues

Datasets:

On BioConductor:mosdef-1.9.0(bioc 3.24)mosdef-1.8.0(bioc 3.23)

geneexpressionsoftwaretranscriptiontranscriptomicsdifferentialexpressionvisualizationreportwritinggenesetenrichmentgo

5.56 score 4 packages 1 scripts 518 downloads 28 exports 174 dependencies

Last updated from:be5ac3c55d. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING326
linux-devel-x86_64NOTE803
source / vignettesOK671
linux-release-x86_64NOTE694
macos-release-arm64NOTE509
macos-oldrel-arm64NOTE429
windows-develNOTE825
windows-releaseNOTE747
windows-oldrelNOTE697
wasm-releaseOK328

Exports:buttonifiercreate_link_dbPTMcreate_link_ENSEMBLcreate_link_GeneCardscreate_link_GOcreate_link_GTEXcreate_link_HPAcreate_link_NCBIcreate_link_PubMedcreate_link_UniProtde_table_painterde_volcanoderesult_to_dfgene_plotgeneinfo_to_htmlget_annotation_orgdbget_expr_valuesgo_to_htmlgo_volcanomap_to_colormosdef_de_container_checkmosdef_res_checkpair_corrplot_marun_cluProrun_goseqrun_topGOstyleColorBar_divergent

Dependencies:abindaisdkAnnotationDbiapeaplotaskpassbase64encBHBiasedUrnBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcachemcallrcigarillocliclusterclusterProfilercodetoolscpp11crayoncrosstalkcurlDBIdbplyrDelayedArrayDESeq2digestDOSEdplyrDTenrichitenrichplotevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverformatRfsfutile.loggerfutile.optionsgdtoolsgeneLenDataBasegenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgoseqgraphgridGraphicsgsongtablehighrhmshtmltoolshtmlwidgetshttrhttr2igraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslotelpatchworkpillarpkgconfigplyrpngpolyclipprettyunitsprocessxprogresspromisespspurrrqvalueR6rappdirsRColorBrewerRcppRcppArmadilloRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesscatterpieSeqinfosnowSparseArraySparseMstringistringrSummarizedExperimentsyssystemfontstibbletidydrtidyrtidyselecttidytreetinytextopGOtreeiotweenrtxdbmakerUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxml2XVectoryamlyulab.utils

The mosdef User's Guide

Leon Dammer, Federico Marini

Rendered frommosdef_userguide.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2024-09-13
Started: 2021-10-01

Readme and manuals

Help Manual

Help pageTopics
Printing some info before the enrichment runs.info_enrichrun
Create sets of buttons for gene symbolsbuttonifier
Link to dbPTM databasecreate_link_dbPTM
Link to ENSEMBL databasecreate_link_ENSEMBL
Link to the GeneCards databasecreate_link_GeneCards
Link to AMIGO databasecreate_link_GO
Link to the GTEx Portalcreate_link_GTEX
Link to the Human Protein Atlascreate_link_HPA
Link to NCBI databasecreate_link_NCBI
Link to Pubmedcreate_link_PubMed
Link to UniProt databasecreate_link_UniProt
DE table painterde_table_painter
Generates a volcano plot using ggplot2de_volcano
Generate a table from the 'DESeq2' resultsderesult_to_df
Plot expression values for a genegene_plot
Information on a genegeneinfo_to_html
Get an annotation data frame from org db packagesget_annotation_orgdb
Get expression valuesget_expr_values
Information on a Gene Ontology identifiergo_to_html
Generates a volcano plot using ggplot2 This function generates a base volcano plot highlighting genes associated with a certain GOterm that can then be expanded upon using further ggplot functions.go_volcano
Maps numeric values to color valuesmap_to_color
A function checking if your 'de_container' contains everything you needmosdef_de_container_check
A function checking if your res_de contains everything you needmosdef_res_check
Pairwise scatter plot matrix and correlation plot of countspair_corr
MA-plot from base means and log fold changesplot_ma
A sample enrichment objectres_enrich_macrophage_cluPro
A sample enrichment objectres_enrich_macrophage_goseq
A sample enrichment objectres_enrich_macrophage_topGO
A sample 'DESeqResults' objectres_macrophage_IFNg_vs_naive
Extract functional terms enriched in the DE genes, based on clusterProfilerrun_cluPro
Extract functional terms enriched in the DE genes, based on goseqrun_goseq
Extract functional terms enriched in the DE genes, based on topGOrun_topGO
Style DT color barsstyleColorBar_divergent