ccfindR

DOI: 10.18129/B9.bioc.ccfindR    

Cancer Clone Finder

Bioconductor version: Release (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>

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

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
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

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