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:Lars Bosshard [aut, cre], Michael Prummer [aut]

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-4.5-any)scROSHI_1.0.0.0.tgz(r-4.4-any)scROSHI_1.0.0.0.tgz(r-4.3-any)
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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'))
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.70 score 9 scripts 167 downloads 6 exports 42 dependencies

Last updated 2 years agofrom:e2fed0e27e. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 13 2025
R-4.5-winOKMar 13 2025
R-4.5-macOKMar 13 2025
R-4.5-linuxOKMar 13 2025
R-4.4-winOKMar 13 2025
R-4.4-macOKMar 13 2025
R-4.4-linuxOKMar 13 2025
R-4.3-winOKMar 13 2025
R-4.3-macOKMar 13 2025

Exports:f_annot_ctgenesf_my_correlation_testf_my_wilcox_testf_score_ctgenes_Uf_score_profile_corscROSHI

Dependencies:abindaskpassBHBiobaseBiocGenericscrayoncurlDelayedArraydqrngFNNgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesirlbajsonlitelatticelimmaMatrixMatrixGenericsmatrixStatsmimeopensslR6RcppRcppAnnoyRcppEigenRcppProgressRSpectraS4ArraysS4VectorsSingleCellExperimentsitmoSparseArraystatmodSummarizedExperimentsysUCSC.utilsuwotXVector