cellTree
This package is for version 3.8 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: 3.8
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("cellTree")):
Installation
To install this package, start R (version "3.5") 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 | 1.12.1 |
| 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_1.12.1.tar.gz |
| Windows Binary | cellTree_1.12.1.zip |
| Mac OS X 10.11 (El Capitan) | cellTree_1.12.1.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 3.8 | Source Archive |