Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
| Version: | 1.5.2 |
| Depends: | R (≥ 3.5.0),Matrix,igraph |
| Imports: | abind,cowplot,ComplexHeatmap,dendextend,dplyr,ggplot2,ggrepel,gridExtra,irlba,leidenAlg,magrittr, methods,N2R, parallel,R6,reshape2,rlang,Rtsne,sccore (≥ 1.0.0), stats, tools, utils |
| LinkingTo: | Rcpp,RcppArmadillo,RcppEigen,RcppProgress |
| Suggests: | AnnotationDbi,BiocParallel, conosPanel,drat,DESeq2,entropy,ggrastr,GO.db,jsonlite,knitr,org.Hs.eg.db,org.Mm.eg.db, p2data,pagoda2,PMA,plyr,rhdf5,rmarkdown,rmumps,Seurat,shinycssloaders,SummarizedExperiment,testthat,tibble,uwot,zoo |
| Published: | 2024-02-26 |
| DOI: | 10.32614/CRAN.package.conos |
| Author: | Viktor Petukhov [aut], Nikolas Barkas [aut], Peter Kharchenko [aut], Weiliang Qiu [ctb], Evan Biederstedt [aut, cre] |
| Maintainer: | Evan Biederstedt <evan.biederstedt at gmail.com> |
| BugReports: | https://github.com/kharchenkolab/conos/issues |
| License: | GPL-3 |
| Copyright: | See the file COPYRIGHTS for various conos copyright details
conos copyright details |
| URL: | https://github.com/kharchenkolab/conos |
| NeedsCompilation: | yes |
| Additional_repositories: | https://kharchenkolab.github.io/drat/ |
| Materials: | README |
| In views: | Omics |
| CRAN checks: | conos results |