cellTree

This package is for version 3.13 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: 3.13

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

Details

biocViews BiomedicalInformatics, CellBiology, Clustering, FunctionalGenomics, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse, Visualization
Version 1.22.0
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
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package cellTree_1.22.0.tar.gz
Windows Binary cellTree_1.22.0.zip
macOS 10.13 (High Sierra) cellTree_1.22.0.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 3.13 Source Archive