cellTree

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see cellTree.

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


Bioconductor version: 3.9

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 (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cellTree")

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

Details

biocViews BiomedicalInformatics, CellBiology, Clustering, FunctionalGenomics, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse, Visualization
Version 1.14.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License Artistic-2.0
Depends R (>= 3.3), topGO
Imports topicmodels, slam, maptpx, igraph, xtable, gplots
System Requirements
URL http://tsudalab.org
See More
Suggests BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db, Biobase, tools
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package cellTree_1.14.0.tar.gz
Windows Binary cellTree_1.14.0.zip
Mac OS X 10.11 (El Capitan) cellTree_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cellTree
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cellTree
Bioc Package Browser https://code.bioconductor.org/browse/cellTree/
Package Short Url https://bioconductor.org/packages/cellTree/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive