{"Package":"tmod","Type":"Package","Title":"Feature Set Enrichment Analysis for Metabolomics and\nTranscriptomics","Version":"0.50.13","Authors@R":"person(given = \"January\",\nfamily = \"Weiner\",\nrole = c(\"aut\", \"cre\"),\nemail = \"january.weiner@gmail.com\",\ncomment = c(ORCID = \"0000-0003-1438-7819\"))","Maintainer":"January Weiner ","Description":"Methods and feature set definitions for feature or gene set\nenrichment analysis in transcriptional and metabolic profiling data.\nPackage includes tests for enrichment based on ranked lists of features,\nfunctions for visualisation and multivariate functional analysis. See Zyla et al (2019)\n.","URL":"https://tmod.online, https://github.com/january3/tmod/,\nhttps://january3.github.io/tmod/","License":"GPL (>= 2.0)","Depends":"R (>= 2.10)","LazyData":"false","VignetteBuilder":"knitr","Imports":"beeswarm,tagcloud,XML,methods,plotwidgets,RColorBrewer,gplots,tibble,pheatmap,ggplot2,tidyr,purrr,rlang,tidyselect,ggrepel","Suggests":"testthat,knitr,rmarkdown,dplyr,pander,cowplot","RoxygenNote":"7.2.0","Encoding":"UTF-8","NeedsCompilation":"no","Packaged":"2023-03-31 11:39:20 UTC; january","Author":"January Weiner [aut, cre] ()","Repository":"CRAN","Date/Publication":"2023-03-31 12:50:02 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/tmod_0.50.13.tar.gz","jsonAuthors":[{"name":"January Weiner","email":"january.weiner@gmail.com","maintainer":true}],"readme":"\n\n\n# tmod

\n\n\n\n[![R-CMD-check](https://github.com/january3/tmod/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/january3/tmod/actions/workflows/R-CMD-check.yaml)\n[![test-coverage](https://github.com/january3/tmod/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/january3/tmod/actions/workflows/test-coverage.yaml)\n[![CRAN\nstatus](https://www.r-pkg.org/badges/version/tmod)](https://CRAN.R-project.org/package=tmod)\n\n\nTmod is a suite of gene set enrichment algorithms, visualizations and\nutilities which comes bundled with a few libraries of gene sets\n(“modules”). Following features distinguish tmod from other packages:\n\n- “panel plot” visualizations which allow to compare results of gene\n set enrichments;\n- several enrichment algorithms are implemented in tmod, in particular\n the very efficient, versatile and\n [reproducible](https://academic.oup.com/bioinformatics/article/35/24/5146/5511403)\n algorithm called “CERNO”;\n- it includes a library of gene sets derived from clustering of gene\n expression data from human blood, which is especially useful in\n functional analysis in infection and immune responses.\n\n## Installation\n\nYou can install the released version of tmod from\n[CRAN](https://CRAN.R-project.org/) with:\n\n``` r\ninstall.packages(\"tmod\")\n```\n\nAnd the development version from [GitHub](https://github.com/) with:\n\n``` r\n# install.packages(\"devtools\")\ndevtools::install_github(\"january3/tmod\")\n```\n\n## Tmod manual\n\n- Access the documentation using `vignette(\"tmod\")`\n- Full user manual is found\n [here](https://january3.github.io/tmod/articles/user_manual/tmod_user_manual.html)\n\n## Example usage\n\n``` r\nlibrary(tmod)\n#> For tmod user guide, type `vignette(\"tmod\")`\ndata(EgambiaResults)\ntt <- EgambiaResults\n\n## gene set enrichment analysis\nres <- tmodCERNOtest(tt$GENE_SYMBOL)\nhead(res)\n#> ID Title cerno N1 AUC\n#> LI.M37.0 LI.M37.0 immune activation - generic cluster 426.3578 100 0.7462103\n#> DC.M4.2 DC.M4.2 Inflammation 151.1520 20 0.9503953\n#> DC.M3.4 DC.M3.4 Interferon 129.4727 17 0.8315780\n#> DC.M1.2 DC.M1.2 Interferon 112.7056 17 0.9004196\n#> DC.M7.29 DC.M7.29 Undetermined 118.6759 20 0.8087599\n#> LI.M11.0 LI.M11.0 enriched in monocytes (II) 113.8086 20 0.7766542\n#> cES P.Value adj.P.Val\n#> LI.M37.0 2.131789 1.824844e-18 1.105856e-15\n#> DC.M4.2 3.778799 8.040039e-15 2.436132e-12\n#> DC.M3.4 3.808019 4.609405e-13 9.310998e-11\n#> DC.M1.2 3.314869 2.298170e-10 3.481728e-08\n#> DC.M7.29 2.966897 1.002268e-09 1.214749e-07\n#> LI.M11.0 2.845216 5.255069e-09 5.307620e-07\n```","jobInfo":{"package":"tmod","version":"0.50.13","parsingStatus":"success","parserVersion":2,"parsedAt":"2023-03-31T15:30:23+0000"}}

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