DOI: 10.18129/B9.bioc.cellTree    

This package is for version 3.8 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: 3.8

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")):


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


biocViews BiomedicalInformatics, CellBiology, Clustering, FunctionalGenomics, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse, Visualization
Version 1.12.1
In Bioconductor since BioC 3.3 (R-3.3) (3 years)
License Artistic-2.0
Depends R (>= 3.3), topGO
Imports topicmodels, slam, maptpx, igraph, xtable, gplots
Suggests BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db, Biobase, tools
URL http://tsudalab.org
Depends On Me
Imports Me
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Source Package cellTree_1.12.1.tar.gz
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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 http://bioconductor.org/packages/cellTree/
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