cellTree

This package is for version 3.14 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

DOI: 10.18129/B9.bioc.cellTree

Bioconductor version: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BiomedicalInformatics, CellBiology, Clustering, FunctionalGenomics, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse, Visualization

Version 1.24.0

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

Suggests BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db, Biobase, tools

Linking To

Enhances

Depends On 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_1.24.0.tar.gz

Windows Binary cellTree_1.24.0.zip

macOS 10.13 (High Sierra) cellTree_1.24.0.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 3.14 Source Archive