Package: hacksig 0.2.0
hacksig: A Tidy Framework to Hack Gene Expression Signatures
A collection of cancer transcriptomics gene signatures as well as a simple and tidy interface to compute single sample enrichment scores either with the original procedure or with three alternatives: the "combined z-score" of Lee et al. (2008) <doi:10.1371/journal.pcbi.1000217>, the "single sample GSEA" of Barbie et al. (2009) <doi:10.1038/nature08460> and the "singscore" of Foroutan et al. (2018) <doi:10.1186/s12859-018-2435-4>. The 'get_sig_info()' function can be used to retrieve information about each signature implemented.
Authors:
hacksig_0.2.0.tar.gz
hacksig_0.2.0.zip(r-4.5)hacksig_0.2.0.zip(r-4.4)hacksig_0.2.0.zip(r-4.3)
hacksig_0.2.0.tgz(r-4.5-any)hacksig_0.2.0.tgz(r-4.4-any)hacksig_0.2.0.tgz(r-4.3-any)
hacksig_0.2.0.tar.gz(r-4.5-noble)hacksig_0.2.0.tar.gz(r-4.4-noble)
hacksig_0.2.0.tgz(r-4.4-emscripten)hacksig_0.2.0.tgz(r-4.3-emscripten)
hacksig.pdf |hacksig.html✨
hacksig/json (API)
NEWS
| # Install 'hacksig' in R: |
| install.packages('hacksig', repos = c('https://acare.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/acare/hacksig/issues
Pkgdown site:https://acare.github.io
- test_expr - A toy gene expression matrix
gene-expression-signaturesgene-set-enrichment
Last updated 2 years agofrom:0b199bf66e. Checks:4 OK, 4 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 27 2025 |
| R-4.5-win | OK | Jan 27 2025 |
| R-4.5-mac | OK | Jan 27 2025 |
| R-4.5-linux | OK | Jan 27 2025 |
| R-4.4-win | NOTE | Jan 27 2025 |
| R-4.4-mac | NOTE | Jan 27 2025 |
| R-4.3-win | NOTE | Jan 27 2025 |
| R-4.3-mac | NOTE | Jan 27 2025 |
Exports:check_sigget_sig_genesget_sig_infohack_cinsarchack_estimatehack_immunophenoscorehack_sigstratify_sig
Dependencies:clicodetoolsdata.tabledigestfansifuturefuture.applyglobalsgluelifecyclelistenvmagrittrparallellypillarpkgconfigrlangtibbleutf8vctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Check signatures feasibility | check_sig |
| Get signature gene identifiers | get_sig_genes |
| Display available gene signatures | get_sig_info |
| Hack the CINSARC classification | hack_cinsarc |
| Hack the ESTIMATE scores | hack_estimate |
| Hack the Immunophenoscore | hack_immunophenoscore |
| Score samples by gene signatures | hack_sig |
| Stratify samples into classes | stratify_sig |
| A toy gene expression matrix | test_expr |
