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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 |
Reference manual: | conos.pdf |
Package source: | conos_1.5.2.tar.gz |
Windows binaries: | r-devel: conos_1.5.2.zip, r-release: conos_1.5.2.zip, r-oldrel: conos_1.5.2.zip |
macOS binaries: | r-release (arm64): conos_1.5.2.tgz, r-oldrel (arm64): conos_1.5.0.tgz, r-release (x86_64): conos_1.5.2.tgz, r-oldrel (x86_64): conos_1.5.2.tgz |
Old sources: | conos archive |
Reverse suggests: | CRMetrics, scITD |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.