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: | 1.4.3 |
| Depends: | R (≥ 3.5.0), Matrix, igraph |
| Imports: | abind, cowplot, ComplexHeatmap, dendextend, dplyr, ggplot2, ggrepel, gridExtra, irlba, leidenAlg, magrittr, Matrix.utils, methods, N2R, parallel, R6, reshape2, rlang, Rtsne, sccore (> 0.1.2), 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, pbapply, PMA, pROC, plyr, rhdf5, rmarkdown, rmumps, Seurat, shinycssloaders, SummarizedExperiment, testthat, tibble, uwot, zoo |
| Published: | 2021-08-07 |
| 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 |
| CRAN checks: | conos results |
| Reference manual: | conos.pdf |
| Package source: | conos_1.4.3.tar.gz |
| Windows binaries: | r-devel: conos_1.4.3.zip, r-devel-UCRT: conos_1.4.3.zip, r-release: conos_1.4.3.zip, r-oldrel: conos_1.4.3.zip |
| macOS binaries: | r-release (arm64): not available, r-release (x86_64): conos_1.4.3.tgz, r-oldrel: conos_1.4.3.tgz |
| Old sources: | conos archive |
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