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:
scCATCH_3.2.2.tar.gz
scCATCH_3.2.2.zip(r-4.5)scCATCH_3.2.2.zip(r-4.4)scCATCH_3.2.2.zip(r-4.3)
scCATCH_3.2.2.tgz(r-4.4-any)scCATCH_3.2.2.tgz(r-4.3-any)
scCATCH_3.2.2.tar.gz(r-4.5-noble)scCATCH_3.2.2.tar.gz(r-4.4-noble)
scCATCH_3.2.2.tgz(r-4.4-emscripten)scCATCH_3.2.2.tgz(r-4.3-emscripten)
scCATCH.pdf |scCATCH.html✨
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
cell-markerscluster-annotationmarker-genesrna-seqsequencingseuratsingle-celltranscriptometranscriptomics
Last updated 2 years agofrom:06c6ffb960. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 29 2024 |
| R-4.5-win | OK | Oct 29 2024 |
| R-4.5-linux | OK | Oct 29 2024 |
| R-4.4-win | NOTE | Oct 29 2024 |
| R-4.4-mac | NOTE | Oct 29 2024 |
| R-4.3-win | OK | Oct 29 2024 |
| R-4.3-mac | OK | Oct 29 2024 |
Exports:createscCATCHdemo_datademo_geneinfodemo_markerfindcelltypefindmarkergenerev_gene
Dependencies:clicrayongluehmslatticelifecyclemagrittrMatrixpkgconfigplyrprettyunitsprogressR6Rcppreshape2rlangstringistringrvctrs
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 |
