DOI: 10.18129/B9.bioc.ccfindR    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see ccfindR.

Cancer Clone Finder

Bioconductor version: 3.7

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

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

Maintainer: Jun Woo <jwoo at>

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PDF R Script ccfindR: single-cell RNA-seq clustering with non-negative matrix factorization
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Text   NEWS


biocViews Bayesian, Clustering, SingleCell, Software, Transcriptomics
Version 1.0.0
License GPL (>= 2)
Depends R (>= 3.5.0)
Imports stats, S4Vectors, BiocGenerics, utils, methods, Matrix, SummarizedExperiment, SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape
Suggests knitr, rmarkdown
Depends On Me
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