Package: MicrobiomeProfiler 1.13.0

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]

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MicrobiomeProfiler.pdf |MicrobiomeProfiler.html✨
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:

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
microbiota_taxlist - Example data: a vector of 54 bacterial genera tested for significantly between T2D metformin samples

On BioConductor:MicrobiomeProfiler-1.11.1(bioc 3.20)MicrobiomeProfiler-1.10.0(bioc 3.19)

microbiome software visualization kegg

6.69 score 36 stars 18 scripts 247 downloads 8 exports 145 dependencies

Last updated 20 days agofrom:2233f8ac5f. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	OK	Oct 31 2024
R-4.5-linux	OK	Oct 30 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

Exports:enrichCOG enrichHMDB enrichKO enrichMBKEGG enrichMDA enrichModule enrichSMPDB run_MicrobiomeProfiler

Dependencies:AnnotationDbi ape aplot askpass attempt base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob bslib cachem cli clusterProfiler codetools colorspace commonmark config cowplot cpp11 crayon crosstalk curl data.table DBI digest DOSE dplyr DT enrichplot evaluate fansi farver fastmap fastmatch fgsea fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData ggforce ggfun ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db golem GOSemSim gridGraphics gson gtable here highr htmltools htmlwidgets httpuv httr igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl patchwork pillar pkgconfig plogr plyr png polyclip promises purrr qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen reshape2 rlang rmarkdown rprojroot RSQLite S4Vectors sass scales scatterpie shiny shinycustomloader shinyWidgets snow sourcetools stringi stringr sys systemfonts tibble tidyr tidyselect tidytree tinytex treeio tweenr UCSC.utils utf8 vctrs viridisLite withr xfun xtable XVector yaml yulab.utils zlibbioc

Introduction to MicrobiomeProfiler

Meijun Chen and GuangChuang Yu

Rendered fromMicrobiomeProfiler.Rmdusingknitr::rmarkdownon Oct 30 2024.

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
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