Package: sccca 0.1.1

sccca: Single-Cell Correlation Based Cell Type Annotation

Performing cell type annotation based on cell markers from a unified database. The approach utilizes correlation-based approach combined with association analysis using Fisher-exact and phyper statistical tests (Upton, Graham JG. (1992) <doi:10.2307/2982890>).

Authors:Mohamed Soudy [aut, cre], Sophie LE BARS [aut], Enrico Glaab [aut]

sccca_0.1.1.tar.gz
sccca_0.1.1.zip(r-4.7)sccca_0.1.1.zip(r-4.6)sccca_0.1.1.zip(r-4.5)
sccca_0.1.1.tgz(r-4.6-any)sccca_0.1.1.tgz(r-4.5-any)
sccca_0.1.1.tar.gz(r-4.7-any)sccca_0.1.1.tar.gz(r-4.6-any)
sccca_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
sccca/json (API)

# Install 'sccca' in R:

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

On CRAN:

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

1.00 score 1 stars 157 downloads 14 exports 146 dependencies

Last updated from:bb077ac514. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	222
source / vignettes	OK	246
linux-release-x86_64	OK	270
macos-release-arm64	OK	136
macos-oldrel-arm64	OK	114
windows-devel	OK	174
windows-release	OK	172
windows-oldrel	OK	189
wasm-release	OK	161

Exports:calculate_cor_mat calculate_normalized_ratio correct_gene_symbols enrich_genes filter_correlation filter_list fisher_test match_characters phyper_test process_clus process_database process_markers sccca sctype

Dependencies:abind askpass base64enc BH bitops bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crosstalk curl data.table deldir digest dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here HGNChelper highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix matrixStats memoise mime miniUI nlme openssl openxlsx otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S7 sass scales scattermore sctransform Seurat SeuratObject shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils splitstackshape stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable yaml zip zoo

Citation

Readme and manuals

Help Manual

Help page	Topics
Performs aggregation based on cell clusters and condition. Then, it calculates correlation matrix of genes	calculate_cor_mat
Calculate cell scores based on number of genes	calculate_normalized_ratio
Process the cell markers names	correct_gene_symbols
Performs parallel function on two lists	enrich_genes
Filter the genes based on specific correlation threshold	filter_correlation
Process the cell markers that overlap between the cell markers and scRNA matrix	filter_list
Performs fisher exact test to get the significant overlap between genes for cell type assignment	fisher_test
Process the cell markers that pass specific threshold in the gene correlation matrix	match_characters
Performs phyper test to get the significant overlap between genes for cell type assignment	phyper_test
Gets the associated cell types using correlation-based approach	process_clus
Process the database for the sctype approach	process_database
Process the cell markers database and return the processed list	process_markers
Run the pipeline for the cell type assignment	sccca
Run the sctype approach as it's implemented by Ianevski, A., Giri, A.K. and Aittokallio, T.	sctype

Package: sccca 0.1.1

sccca: Single-Cell Correlation Based Cell Type Annotation

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)