Package: ImmuneSigR 0.1.0
Yingyan Liang
ImmuneSigR: Immune Cell Signature Retrieval and Single-Cell Scoring
Provides a literature-derived database of immune cell markers formatted as Gene Matrix Transposed (GMT) files. Users can search immune cell signatures, retrieve marker lists, export GMT files, create custom marker sets, and score gene-by-cell expression matrices with dependency-free rank-based or mean-expression methods. Cell subpopulations are distinguished by their source PMIDs. For the core curation of the lung cell atlas, see Travaglini et al. (2020) <doi:10.1038/s41586-020-2922-4>. For the pan-cancer B cell signatures, see Fitzsimons et al. (2024) <doi:10.1016/j.ccell.2024.09.011>.
Authors:
ImmuneSigR_0.1.0.tar.gz
ImmuneSigR_0.1.0.tar.gz(r-4.7-any)ImmuneSigR_0.1.0.tar.gz(r-4.6-any)
ImmuneSigR_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ImmuneSigR/json (API)
NEWS
| # Install 'ImmuneSigR' in R: |
| install.packages('ImmuneSigR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yingyanlaing/immunesigr/issues
Last updated from:33f22c3165. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 113 | ||
| source / vignettes | OK | 182 | ||
| linux-release-x86_64 | OK | 116 | ||
| wasm-release | OK | 90 |
Exports:Create_Custom_GMTExport_GMTExport_ImmuneSigR_GMTGet_MarkersScore_CellSigRScore_ImmuneSigRSearch_CellSigRSearch_ImmuneSigR
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create a Custom GMT File | Create_Custom_GMT |
| Export the built-in GMT file | Export_GMT Export_ImmuneSigR_GMT |
| Get Marker Genes for Specific Cell Types | Get_Markers |
| Score Expression Data using ImmuneSigR | Score_CellSigR Score_ImmuneSigR |
| Search the ImmuneSigR Database | Search_CellSigR Search_ImmuneSigR |
