cellTree

DOI: 10.18129/B9.bioc.cellTree  

This package is for version 3.16 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: Release (3.16)

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 "4.2") 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 1.27.0
In Bioconductor since BioC 3.3 (R-3.3) (7 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_1.27.0.tar.gz
Windows Binary cellTree_1.27.0.zip
macOS Binary (x86_64) cellTree_1.27.0.tgz
macOS Binary (arm64)
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

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