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:	1.5.2
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
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

Documentation:

Reference manual:

conos.pdf

Downloads:

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 dependencies:

Reverse suggests:

CRMetrics, scITD

Linking:

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