Package: scROSHI 1.0.0.1
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: Michael Prummer, Anne Bertolini, Lars Bosshard, Florian Barkmann, Josephine Yates, Valentina Boeva, The Tumor Profiler Consortium , Daniel Stekhoven, Franziska Singer, scROSHI: robust supervised hierarchical identification of single cells, NAR Genomics and Bioinformatics, Volume 5, Issue 2, June 2023, lqad058, <doi:10.1093/nargab/lqad058>.
Authors:
scROSHI_1.0.0.1.tar.gz
scROSHI_1.0.0.1.zip(r-4.7-any)scROSHI_1.0.0.1.zip(r-4.6-any)scROSHI_1.0.0.1.zip(r-4.5-any)
scROSHI_1.0.0.1.tgz(r-4.6-any)scROSHI_1.0.0.1.tgz(r-4.5-any)
scROSHI_1.0.0.1.tar.gz(r-4.7-any)scROSHI_1.0.0.1.tar.gz(r-4.6-any)
scROSHI_1.0.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
scROSHI/json (API)
| # Install 'scROSHI' in R: |
| install.packages('scROSHI', repos = c('https://dominikburri.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 from:569f7f592f. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 135 | ||
| source / vignettes | OK | 156 | ||
| linux-release | OK | 135 | ||
| macos-release | OK | 155 | ||
| macos-oldrel | OK | 182 | ||
| windows-devel | OK | 123 | ||
| windows-release | OK | 85 | ||
| windows-oldrel | OK | 88 | ||
| wasm-release | OK | 106 |
Exports:f_annot_ctgenesf_my_correlation_testf_my_wilcox_testf_score_ctgenes_Uf_score_profile_corscROSHI
Dependencies:abindBHBiobaseBiocGenericsDelayedArraydqrngFNNgenericsGenomicRangesIRangesirlbalatticelimmaMatrixMatrixGenericsmatrixStatsRcppRcppAnnoyRcppEigenRcppProgressRSpectraS4ArraysS4VectorsSeqinfoSingleCellExperimentsitmoSparseArraystatmodSummarizedExperimentuwotXVector
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-package scROSHI |
| Test SCE Data Set | test_sce_data |