Package: scCATCH 3.2.2

Xin Shao

scCATCH: Single Cell Cluster-Based Annotation Toolkit for Cellular Heterogeneity

An automatic cluster-based annotation pipeline based on evidence-based score by matching the marker genes with known cell markers in tissue-specific cell taxonomy reference database for single-cell RNA-seq data. See Shao X, et al (2020) <doi:10.1016/j.isci.2020.100882> for more details.

Authors:Xin Shao

scCATCH_3.2.2.tar.gz
scCATCH_3.2.2.zip(r-4.7)scCATCH_3.2.2.zip(r-4.6)scCATCH_3.2.2.zip(r-4.5)
scCATCH_3.2.2.tgz(r-4.6-any)scCATCH_3.2.2.tgz(r-4.5-any)
scCATCH_3.2.2.tar.gz(r-4.7-any)scCATCH_3.2.2.tar.gz(r-4.6-any)
scCATCH_3.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
scCATCH/json (API)

# Install 'scCATCH' in R:

install.packages('scCATCH', repos = c('https://zjufanlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zjufanlab/sccatch/issues

Datasets:

cellmatch - Cellmatch
geneinfo - Geneinfo

On CRAN:

cell-markers cluster-annotation marker-genes rna-seq sequencing seurat single-cell transcriptome transcriptomics

7.39 score 241 stars 126 scripts 390 downloads 4 mentions 7 exports 19 dependencies

Last updated from:06c6ffb960. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	141
source / vignettes	OK	173
linux-release-x86_64	OK	139
macos-release-arm64	OK	174
macos-oldrel-arm64	OK	236
windows-devel	OK	95
windows-release	OK	88
windows-oldrel	OK	105
wasm-release	OK	111

Exports:createscCATCH demo_data demo_geneinfo demo_marker findcelltype findmarkergene rev_gene

Dependencies:cli crayon glue hms lattice lifecycle magrittr Matrix pkgconfig plyr prettyunits progress R6 Rcpp reshape2 rlang stringi stringr vctrs

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
cellmatch	cellmatch
scCATCH object	createscCATCH
Demo data of single-cell RNA-seq data	demo_data
Demo data of geneinfo	demo_geneinfo
Demo data of markers	demo_marker
Evidence-based score and annotation for each cluster	findcelltype
Find potential marker genes for each cluster	findmarkergene
geneinfo	geneinfo
Pre-processing step: revising gene symbols	rev_gene
Definition of 'scCATCH' class	scCATCH scCATCH-class