ccfindR

DOI: 10.18129/B9.bioc.ccfindR    

Cancer Clone Finder

Bioconductor version: Release (3.8)

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 umn.edu>

Citation (from within R, enter citation("ccfindR")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ccfindR", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ccfindR")

 

HTML R Script ccfindR: single-cell RNA-seq analysis using Bayesian non-negative matrix factorization
PDF   Reference Manual
Text   NEWS

Details

biocViews Bayesian, Clustering, SingleCell, Software, Transcriptomics
Version 1.2.0
License GPL (>= 2)
Depends R (>= 3.5.1)
Imports stats, S4Vectors, utils, methods, Matrix, SummarizedExperiment, SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp
LinkingTo Rcpp, RcppEigen
Suggests BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ccfindR_1.2.0.tar.gz
Windows Binary ccfindR_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) ccfindR_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ccfindR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ccfindR
Package Short Url http://bioconductor.org/packages/ccfindR/
Package Downloads Report Download Stats

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