Installation | Setup | getting gene-profile from a file | getting gene-sets from msigdbr | Running the analysis with alternative = "two.sided" | The summary method. | Trimming the table fo results | Plotting the analysis | A more intensive analysis: playing with more than 10,000 gene-sets | Session info
Package: massiveGST 1.0.1
Stefano Maria Pagnotta
massiveGST: Competitive Gene Sets Test with the Mann-Whitney-Wilcoxon Test
Friendly implementation of the Mann-Whitney-Wilcoxon test for competitive gene set enrichment analysis.
Authors:
massiveGST_1.0.1.tar.gz
massiveGST_1.0.1.zip(r-4.7-any)massiveGST_1.0.1.zip(r-4.6-any)massiveGST_1.0.1.zip(r-4.5-any)
massiveGST_1.0.1.tgz(r-4.6-any)massiveGST_1.0.1.tgz(r-4.5-any)
massiveGST_1.0.1.tar.gz(r-4.7-any)massiveGST_1.0.1.tar.gz(r-4.6-any)
massiveGST_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
massiveGST/json (API)
| # Install 'massiveGST' in R: |
| install.packages('massiveGST', repos = c('https://stefanomp.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/stefanomp/massivegst/issues
Last updated from:dae27aafa2. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 160 | ||
| source / vignettes | OK | 235 | ||
| linux-release | NOTE | 160 | ||
| macos-release | NOTE | 407 | ||
| macos-oldrel | NOTE | 334 | ||
| windows-devel | NOTE | 139 | ||
| windows-release | NOTE | 92 | ||
| windows-oldrel | NOTE | 113 | ||
| wasm-release | OK | 123 |
Exports:cut_by_logit2NEScut_by_NEScut_by_significanceget_geneProfileget_geneSets_from_local_filesget_geneSets_from_msigdbrmassiveGSTsave_as_tsvsave_as_xlswrite_geneSets_to_gmt
Dependencies:assertthatbabelgenebase64encbslibcachemclicpp11curldigestdplyrevaluatefastmapfontawesomeformattablefsgenericsgluehighrhtmltoolshtmlwidgetsigraphjquerylibjsonliteknitrlatticelifecyclemagrittrMatrixmemoisemimemsigdbrpillarpkgconfigR6rappdirsrlangrmarkdownsasstibbletidyselecttinytexutf8vctrsvisNetworkwithrWriteXLSxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Trim the table of results. | cut_by_logit2NES |
| Trim the table of results. | cut_by_NES |
| Trim the table of results. | cut_by_significance |
| Load a gene-profile from a txt file. | get_geneProfile |
| Load the gene-sets collection from local gmt files | get_geneSets_from_local_files |
| Get the gene-sets from the msigdbr package. | get_geneSets_from_msigdbr |
| massive Gene-Sets Test with Mann-Whitney-Wilcoxon statistics. | massiveGST |
| Graphical rendering of the enrichment analysis. | plot.mGST |
| FGFR3-TACC3 fusion positive gene profile | pre_ranked_list |
| Save the results in tab-separeted value file | save_as_tsv |
| Save the results in xls file format | save_as_xls |
| Generate summary tables | summary.mGST |
| Save a collection of gene-sets in a .gmt file format. | write_geneSets_to_gmt |