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 |