hjunwoo/ccfindR: Cancer Clone Finder

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.

Getting started

Package details

AuthorJun Woo [aut, cre], Jinhua Wang [aut]
Bioconductor views Bayesian Clustering ImmunoOncology SingleCell Transcriptomics
MaintainerJun Woo <[email protected]>
LicenseGPL (>= 2)
Version1.3.0
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("hjunwoo/ccfindR")
hjunwoo/ccfindR documentation built on Dec. 2, 2018, 1:17 a.m.