conos: Clustering on Network of Samples

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: 1.4.0
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 (≥ 0.1.1), stats, tools, utils
LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppProgress
Suggests: AnnotationDbi, BiocParallel, conosPanel, 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: 2021-02-23
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

Downloads:

Reference manual: conos.pdf
Package source: conos_1.4.0.tar.gz
Windows binaries: r-devel: conos_1.4.0.zip, r-release: not available, r-oldrel: not available
macOS binaries: r-release: conos_1.4.0.tgz, r-oldrel: not available

Linking:

Please use the canonical form https://CRAN.R-project.org/package=conos to link to this page.