cellTree
This package is for version 3.9 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: 3.9
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("cellTree")
):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
Reference Manual |
Details
biocViews | BiomedicalInformatics, CellBiology, Clustering, FunctionalGenomics, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse, Visualization |
Version | 1.14.0 |
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_1.14.0.tar.gz |
Windows Binary | cellTree_1.14.0.zip |
Mac OS X 10.11 (El Capitan) | cellTree_1.14.0.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 3.9 | Source Archive |