DOI: 10.18129/B9.bioc.ccfindR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see ccfindR.

Cancer Clone Finder

Bioconductor version: 3.17

A collection of tools for cancer genomic data clustering analyses, including those for single cell RNA-seq. Cell clustering and feature gene selection analysis employ Bayesian (and maximum likelihood) non-negative matrix factorization (NMF) algorithm. Input data set consists of RNA count matrix, gene, and cell bar code annotations. Analysis outputs are factor matrices for multiple ranks and marginal likelihood values for each rank. The package includes utilities for downstream analyses, including meta-gene identification, visualization, and construction of rank-based trees for clusters.

Author: Jun Woo [aut, cre], Jinhua Wang [aut]

Maintainer: Jun Woo <jwoo at>

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biocViews Bayesian, Clustering, ImmunoOncology, SingleCell, Software, Transcriptomics
Version 1.20.0
In Bioconductor since BioC 3.7 (R-3.5) (5.5 years)
License GPL (>= 2)
Depends R (>= 3.6.0)
Imports stats, S4Vectors, utils, methods, Matrix, SummarizedExperiment, SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack (>= 0.7)
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Suggests BiocStyle, knitr, rmarkdown
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