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.


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install.packages("conos")

1.4.5 by Evan Biederstedt, 8 days ago


https://github.com/kharchenkolab/conos


Report a bug at https://github.com/kharchenkolab/conos/issues


Browse source code at https://github.com/cran/conos


Authors: Viktor Petukhov [aut] , Nikolas Barkas [aut] , Peter Kharchenko [aut] , Weiliang Qiu [ctb] , Evan Biederstedt [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports abind, cowplot, ComplexHeatmap, dendextend, dplyr, ggplot2, ggrepel, gridExtra, irlba, leidenAlg, magrittr, Matrix.utils, methods, N2R, parallel, R6, reshape2, rlang, Rtsne, sccore, stats, tools, utils

Depends on Matrix, igraph

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

Linking to Rcpp, RcppArmadillo, RcppEigen, RcppProgress


Suggested by scITD.


See at CRAN