This package is considered a duplicate. The official version of this package is found at:https://cran.r-universe.dev/scaper

Package: scaper 0.2.1

scaper: Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation

Generates cell-level cytokine activity estimates using relevant information from gene sets constructed with the 'CytoSig' and the 'Reactome' databases and scored using the modified 'Variance-adjusted Mahalanobis (VAM)' framework for single-cell RNA-sequencing (scRNA-seq) data. 'CytoSig' database is described in: Jiang at al., (2021) <doi:10.1038/s41592-021-01274-5>. 'Reactome' database is described in: Gillespie et al., (2021) <doi:10.1093/nar/gkab1028>. The 'VAM' method is outlined in: Frost (2020) <doi:10.1093/nar/gkaa582>.

Authors:Zaoqu Liu [aut, cre], H. Robert Frost [aut], Azka Javaid [aut]

scaper_0.2.1.tar.gz
scaper_0.2.1.zip(r-4.7)scaper_0.2.1.zip(r-4.6)scaper_0.2.1.zip(r-4.5)
scaper_0.2.1.tgz(r-4.6-any)scaper_0.2.1.tgz(r-4.5-any)
scaper_0.2.1.tar.gz(r-4.7-any)scaper_0.2.1.tar.gz(r-4.6-any)
scaper_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scaper/json (API)

# Install 'scaper' in R:

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

Bug tracker:https://github.com/zaoqu-liu/scaper/issues

On CRAN:

3.54 score 14 scripts 551 downloads 6 exports 143 dependencies

Last updated from:76fae1d8a4 (on main). Checks:9 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	OK	255
source / vignettes	OK	255
linux-release-x86_64	OK	240
macos-release-arm64	OK	137
macos-oldrel-arm64	OK	139
windows-devel	OK	178
windows-release	OK	175
windows-oldrel	OK	194
wasm-release	OK	205

Exports:%>%genesetCytoSig genesetReactome scape scapeForSeurat supportedCytokines

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 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 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 stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xml2 xtable yaml zoo

Algorithm Details: Mathematical Foundation of scaper

Rendered fromalgorithm-details.Rmdusingknitr::rmarkdown