Package: MicrobiomeProfiler 1.19.1

Guangchuang Yu

MicrobiomeProfiler: An R/shiny package for microbiome functional enrichment analysis

This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.

Authors:Guangchuang Yu [cre, aut], Meijun Chen [aut]

MicrobiomeProfiler_1.19.1.tar.gz
MicrobiomeProfiler_1.19.1.zip(r-4.7)MicrobiomeProfiler_1.19.1.zip(r-4.6)MicrobiomeProfiler_1.19.1.zip(r-4.5)
MicrobiomeProfiler_1.19.1.tgz(r-4.6-any)MicrobiomeProfiler_1.19.1.tgz(r-4.5-any)
MicrobiomeProfiler_1.19.1.tar.gz(r-4.7-any)MicrobiomeProfiler_1.19.1.tar.gz(r-4.6-any)
MicrobiomeProfiler_1.19.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MicrobiomeProfiler/json (API)

# Install 'MicrobiomeProfiler' in R:

install.packages('MicrobiomeProfiler', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yulab-smu/microbiomeprofiler/issues

Datasets:

microbiota_taxlist - Example data: a vector of 54 bacterial genera tested for significantly between T2D metformin samples
Psoriasis_data - Example data: a vector of 134 significantly different functional COGs between Psoriasis patients and controls
Rat_data - Example data: a vector of 91 KEGG Orthologies (KOs) showing significant associations with weaning weight

On BioConductor:MicrobiomeProfiler-1.19.1(bioc 3.24)MicrobiomeProfiler-1.18.1(bioc 3.23)

microbiome software visualization kegg

7.34 score 42 stars 42 scripts 15 exports 136 dependencies

Last updated from:82c128c3ce. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	202
linux-devel-x86_64	NOTE	281
source / vignettes	OK	263
linux-release-x86_64	NOTE	277
macos-release-arm64	NOTE	164
macos-oldrel-arm64	NOTE	130
windows-devel	NOTE	194
windows-release	NOTE	185
windows-oldrel	NOTE	153
wasm-release	OK	158

Exports:enrichCOG enrichHMDB enrichKO enrichMBKEGG enrichMDA enrichModule enrichSMPDB gseCOG gseHMDB gseKO gseMBKEGG gseMDA gseModule gseSMPDB run_MicrobiomeProfiler

Dependencies:aisdk AnnotationDbi ape aplot askpass attempt base64enc Biobase BiocGenerics Biostrings bit bit64 blob bslib cachem callr cli cluster clusterProfiler commonmark config cpp11 crayon crosstalk curl DBI digest DOSE dplyr DT enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db golem GOSemSim gridGraphics gson gtable here highr htmltools htmlwidgets httpuv httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mime nlme openssl otel patchwork pillar pkgconfig plyr png polyclip processx promises ps purrr qvalue R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown rprojroot RSQLite S4Vectors S7 sass scales scatterpie Seqinfo shiny shinycustomloader shinyWidgets sourcetools stringi stringr sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr utf8 vctrs viridisLite withr xfun xtable XVector yaml yulab.utils

Introduction to MicrobiomeProfiler

Rendered fromMicrobiomeProfiler.Rmdusingknitr::rmarkdown

Last update: 2023-04-18
Started: 2021-09-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
COG enrichment analysis for microbiome data	enrichCOG
Metabolism enrichment analysis for microbiome data	enrichHMDB
KO enrichment for microbiome data	enrichKO
Metabolism enrichment analysis for microbiome data	enrichMBKEGG
Microbe-Disease associations enrichment analysis	enrichMDA
Module enrichment for microbiome data	enrichModule
Metabolism enrichment analysis for microbiome data	enrichSMPDB
COG GSEA enrichment analysis for microbiome data	gseCOG
Metabolism GSEA enrichment analysis for microbiome data	gseHMDB
KO GSEA enrichment for microbiome data	gseKO
Metabolism GSEA enrichment analysis for microbiome data	gseMBKEGG
Microbe-Disease associations GSEA enrichment analysis	gseMDA
Module GSEA enrichment for microbiome data	gseModule
Metabolism GSEA enrichment analysis for microbiome data	gseSMPDB
gson_cpd	gson_cpd
gson_enzyme	gson_enzyme
gson_KO	gson_KO
gson_module	gson_module
Example data: a vector of 54 bacterial genera tested for significantly between T2D metformin samples	microbiota_data microbiota_taxlist
Example data: a vector of 134 significantly different functional COGs between Psoriasis patients and controls	Psoriasis_data
Example data: a vector of 91 KEGG Orthologies (KOs) showing significant associations with weaning weight	Rat_data
Run the Shiny Application	run_MicrobiomeProfiler