Core Utilities for Single-Cell RNA-Seq

Core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with differential expression (DE) matrices and count matrices, a collection of functions for manipulating and plotting data via 'ggplot2', and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP , collapsing vertices of each cluster in the graph, and propagating graph labels.


Reference manual

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1.0.0 by Evan Biederstedt, 16 days ago

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Authors: Viktor Petukhov [aut] , Ramus Rydbirk [aut] , Peter Kharchenko [aut] , Evan Biederstedt [aut, cre]

Documentation:   PDF Manual  

GPL-3 license

Imports dplyr, ggplot2, ggrepel, graphics, grDevices, igraph, irlba, magrittr, Matrix, methods, parallel, pbmcapply, pROC, Rcpp, rlang, scales, tibble, utils, uwot, withr

Suggests ggrastr, rmumps, testthat

Linking to Rcpp, RcppArmadillo, RcppProgress, RcppEigen

System requirements: C++11

Imported by conos, leidenAlg, pagoda2.

See at CRAN