cellTree

DOI: 10.18129/B9.bioc.cellTree    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see cellTree.

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

Bioconductor version: 3.14

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>

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")

 

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, ImmunoOncology, Microarray, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse, Visualization
Version	1.24.0
In Bioconductor since	BioC 3.3 (R-3.3) (6 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
Links To Me
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
Package Short Url	https://bioconductor.org/packages/cellTree/
Package Downloads Report	Download Stats