Package: scROSHI 1.0.0.0
scROSHI: Robust Supervised Hierarchical Identification of Single Cells
Identifying cell types based on expression profiles is a pillar of single cell analysis. 'scROSHI' identifies cell types based on expression profiles of single cell analysis by utilizing previously obtained cell type specific gene sets. It takes into account the hierarchical nature of cell type relationship and does not require training or annotated data. A detailed description of the method can be found at: Prummer, Bertolini, Bosshard, Barkmann, Yates, Boeva, The Tumor Profiler Consortium, Stekhoven, and Singer (2022) <doi:10.1101/2022.04.05.487176>.
Authors:
scROSHI_1.0.0.0.tar.gz
scROSHI_1.0.0.0.zip(r-4.5)scROSHI_1.0.0.0.zip(r-4.4)scROSHI_1.0.0.0.zip(r-4.3)
scROSHI_1.0.0.0.tgz(r-4.4-any)scROSHI_1.0.0.0.tgz(r-4.3-any)
scROSHI_1.0.0.0.tar.gz(r-4.5-noble)scROSHI_1.0.0.0.tar.gz(r-4.4-noble)
scROSHI_1.0.0.0.tgz(r-4.4-emscripten)scROSHI_1.0.0.0.tgz(r-4.3-emscripten)
scROSHI.pdf |scROSHI.html✨
scROSHI/json (API)
| # Install 'scROSHI' in R: |
| install.packages('scROSHI', repos = c('https://lbosshard.r-universe.dev', 'https://cloud.r-project.org')) |
- config - Test config file
- marker_list - Marker gene list for the test SCE data Set
- test_sce_data - Test SCE Data Set
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:e2fed0e27e. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 13 2024 |
| R-4.5-win | OK | Oct 13 2024 |
| R-4.5-linux | OK | Oct 13 2024 |
| R-4.4-win | OK | Oct 13 2024 |
| R-4.4-mac | OK | Oct 13 2024 |
| R-4.3-win | OK | Oct 13 2024 |
| R-4.3-mac | OK | Oct 13 2024 |
Exports:f_annot_ctgenesf_my_correlation_testf_my_wilcox_testf_score_ctgenes_Uf_score_profile_corscROSHI
Dependencies:abindaskpassBHBiobaseBiocGenericscrayoncurlDelayedArraydqrngFNNGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesirlbajsonlitelatticelimmaMatrixMatrixGenericsmatrixStatsmimeopensslR6RcppRcppAnnoyRcppEigenRcppProgressRSpectraS4ArraysS4VectorsSingleCellExperimentsitmoSparseArraystatmodSummarizedExperimentsysUCSC.utilsuwotXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Test config file | config |
| Choose best matching cell type | f_annot_ctgenes |
| Spearman correlation test | f_my_correlation_test |
| Wilcox test | f_my_wilcox_test |
| Calculate cell type score | f_score_ctgenes_U |
| Calculate cell type score: U-test | f_score_profile_cor |
| Marker gene list for the test SCE data Set | marker_list |
| Robust Supervised Hierarchical Identification of Single Cells | scROSHI |
| Test SCE Data Set | test_sce_data |
