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>
citation("ccfindR")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ccfindR")
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")| ccfindR: single-cell RNA-seq clustering with non-negative matrix factorization | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, Clustering, SingleCell, Software, Transcriptomics |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.5.0) |
| Imports | stats, S4Vectors, BiocGenerics, utils, methods, Matrix, SummarizedExperiment, SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 | https://bioconductor.org/packages/ccfindR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.7 | Source Archive |