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✨
DESCRIPTION |NEWS
card.svg |card.png
mosdef/json (API)

# 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:

res_enrich_macrophage_cluPro - A sample enrichment object
res_enrich_macrophage_goseq - A sample enrichment object
res_enrich_macrophage_topGO - A sample enrichment object
res_macrophage_IFNg_vs_naive - A sample 'DESeqResults' object

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

geneexpression software transcription transcriptomics differentialexpression visualization reportwriting genesetenrichment go

5.38 score 4 packages 1 scripts 518 downloads 28 exports 175 dependencies

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

Target	Result	Time
bioc-checks	WARNING	372
linux-devel-x86_64	NOTE	788
source / vignettes	OK	670
linux-release-x86_64	NOTE	771
macos-release-arm64	NOTE	428
macos-oldrel-arm64	NOTE	422
windows-devel	NOTE	715
windows-release	NOTE	743
windows-oldrel	NOTE	695
wasm-release	OK	318

Exports:buttonifier create_link_dbPTM create_link_ENSEMBL create_link_GeneCards create_link_GO create_link_GTEX create_link_HPA create_link_NCBI create_link_PubMed create_link_UniProt de_table_painter de_volcano deresult_to_df gene_plot geneinfo_to_html get_annotation_orgdb get_expr_values go_to_html go_volcano map_to_color mosdef_de_container_check mosdef_res_check pair_corr plot_ma run_cluPro run_goseq run_topGO styleColorBar_divergent

Dependencies:abind aisdk AnnotationDbi ape aplot askpass base64enc BH BiasedUrn Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob bslib cachem callr cigarillo cli cluster clusterProfiler codetools cpp11 crayon crosstalk curl DBI dbplyr DelayedArray DESeq2 digest DOSE dplyr DT enrichit enrichplot evaluate farver fastmap filelock fontawesome fontBitstreamVera fontLiberation fontquiver formatR fs futile.logger futile.options gdtools geneLenDataBase generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db GOSemSim goseq graph gridGraphics gson gtable highr hms htmltools htmlwidgets httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl otel patchwork pillar pkgconfig plyr png polyclip prettyunits processx progress promises ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales scatterpie Seqinfo snow SparseArray SparseM stringi stringr SummarizedExperiment sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex topGO treeio tweenr txdbmaker UCSC.utils utf8 vctrs viridisLite withr xfun XML xml2 XVector yaml yulab.utils

The mosdef User's Guide

Rendered frommosdef_userguide.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Printing some info before the enrichment runs	.info_enrichrun
Create sets of buttons for gene symbols	buttonifier
Link to dbPTM database	create_link_dbPTM
Link to ENSEMBL database	create_link_ENSEMBL
Link to the GeneCards database	create_link_GeneCards
Link to AMIGO database	create_link_GO
Link to the GTEx Portal	create_link_GTEX
Link to the Human Protein Atlas	create_link_HPA
Link to NCBI database	create_link_NCBI
Link to Pubmed	create_link_PubMed
Link to UniProt database	create_link_UniProt
DE table painter	de_table_painter
Generates a volcano plot using ggplot2	de_volcano
Generate a table from the 'DESeq2' results	deresult_to_df
Plot expression values for a gene	gene_plot
Information on a gene	geneinfo_to_html
Get an annotation data frame from org db packages	get_annotation_orgdb
Get expression values	get_expr_values
Information on a Gene Ontology identifier	go_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 values	map_to_color
A function checking if your 'de_container' contains everything you need	mosdef_de_container_check
A function checking if your res_de contains everything you need	mosdef_res_check
Pairwise scatter plot matrix and correlation plot of counts	pair_corr
MA-plot from base means and log fold changes	plot_ma
A sample enrichment object	res_enrich_macrophage_cluPro
A sample enrichment object	res_enrich_macrophage_goseq
A sample enrichment object	res_enrich_macrophage_topGO
A sample 'DESeqResults' object	res_macrophage_IFNg_vs_naive
Extract functional terms enriched in the DE genes, based on clusterProfiler	run_cluPro
Extract functional terms enriched in the DE genes, based on goseq	run_goseq
Extract functional terms enriched in the DE genes, based on topGO	run_topGO
Style DT color bars	styleColorBar_divergent