ccfindR

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 umn.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ccfindR")

Documentation

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

browseVignettes("ccfindR")

 

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

Details

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
LinkingTo
Suggests	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_1.0.0.tar.gz
Windows Binary	ccfindR_1.0.0.zip
Mac OS X 10.11 (El Capitan)	ccfindR_1.0.0.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