Package: mosdef 1.3.0

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_1.3.0.tar.gz
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mosdef_1.3.0.tgz(r-4.4-any)mosdef_1.1.3.tgz(r-4.3-any)
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mosdef_1.3.0.tgz(r-4.4-emscripten)mosdef_1.1.3.tgz(r-4.3-emscripten)
mosdef.pdf |mosdef.html✨
mosdef/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:mosdef-1.3.0(bioc 3.21)mosdef-1.2.0(bioc 3.20)

geneexpressionsoftwaretranscriptiontranscriptomicsdifferentialexpressionvisualizationreportwritinggenesetenrichmentgo

6.44 score 4 packages 323 downloads 28 exports 172 dependencies

Last updated 23 days agofrom:6f79161334. Checks:OK: 1 WARNING: 3 NOTE: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-winWARNINGNov 01 2024
R-4.5-linuxWARNINGNov 01 2024
R-4.4-winWARNINGNov 01 2024
R-4.4-macNOTENov 01 2024
R-4.3-winNOTESep 26 2024
R-4.3-macNOTESep 26 2024

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:abindAnnotationDbiapeaplotaskpassbase64encBHBiasedUrnBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcachemcliclusterProfilercodetoolscolorspacecowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDESeq2digestDOSEdplyrDTenrichplotevaluatefansifarverfastmapfastmatchfgseafilelockfontawesomeformatRfsfutile.loggerfutile.optionsgeneLenDataBasegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgoseqgraphgridGraphicsgsongtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrplyrpngpolyclipprettyunitsprogresspromisespurrrqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesscatterpiesnowSparseArraySparseMstringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttidytreetinytextopGOtreeiotweenrtxdbmakerUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxml2XVectoryamlyulab.utilszlibbioc

The mosdef User's Guide

Leon Dammer, Federico Marini

Rendered frommosdef_userguide.Rmdusingknitr::rmarkdownon Nov 01 2024.

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