To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

cellTree

DOI: 10.18129/B9.bioc.cellTree    

Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure

Bioconductor version: Release (3.6)

This packages computes a Latent Dirichlet Allocation (LDA) model of single-cell RNA-seq data and builds a compact tree modelling the relationship between individual cells over time or space.

Author: David duVerle [aut, cre], Koji Tsuda [aut]

Maintainer: David duVerle <dave at cb.k.u-tokyo.ac.jp>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("cellTree")

 

PDF R Script Inference and visualisation of Single-Cell RNA-seq Data data as a hierarchical tree structure
PDF   Reference Manual

Details

biocViews BiomedicalInformatics, CellBiology, Clustering, FunctionalGenomics, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse, Visualization
Version 1.8.0
In Bioconductor since BioC 3.3 (R-3.3) (1.5 years)
License Artistic-2.0
Depends R (>= 3.3), topGO
Imports topicmodels, slam, maptpx, igraph, xtable, gplots
LinkingTo
Suggests BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db, Biobase, tools
SystemRequirements
Enhances
URL http://tsudalab.org
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package cellTree_1.8.0.tar.gz
Windows Binary cellTree_1.8.0.zip
Mac OS X 10.11 (El Capitan) cellTree_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cellTree
Package Short Url http://bioconductor.org/packages/cellTree/
Package Downloads Report Download Stats

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