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

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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]
Date of publication
None
Maintainer
David duVerle <dave@cb.k.u-tokyo.ac.jp>
License
Artistic-2.0
Version
1.4.0
URLs

View on Bioconductor

Man pages

cell.ordering.table
Ranking of cells according to backbone tree structure
cellTree-package
Inference and visualisation of Single-Cell RNA-seq Data data...
compute.backbone.tree
Backbone Tree construction
compute.go.enrichment
Gene Ontology enrichment analysis
compute.lda
LDA model inference
ct.plot.go.dag
Gene Ontology enrichment sets plotting
ct.plot.grouping
Plot cell tree with grouping information
ct.plot.heatmap
Gene Expression Heatmap
ct.plot.topics
Plot cell tree with topic distributions
get.cell.dists
Cell Pairwise-Distance Matrix
go.results.to.latex
LaTeX output for Gene Ontology Enrichment results
HSMM_lda_model
Pre-computed LDA model for HSMMSingleCell data

Files in this package

cellTree/DESCRIPTION
cellTree/NAMESPACE
cellTree/R
cellTree/R/cellTree.R
cellTree/R/private_functions.R
cellTree/R/utils.R
cellTree/REFERENCES.bib
cellTree/build
cellTree/build/vignette.rds
cellTree/data
cellTree/data/HSMM_lda_model.rda
cellTree/examples
cellTree/examples/cell.ordering.table.example.R
cellTree/examples/compute.backbone.tree.example.R
cellTree/examples/compute.go.enrichment.example.R
cellTree/examples/compute.lda.example.R
cellTree/examples/ct.plot.go.dag.example.R
cellTree/examples/ct.plot.grouping.example.R
cellTree/examples/ct.plot.heatmap.example.R
cellTree/examples/ct.plot.topics.example.R
cellTree/examples/get.cell.dists.example.R
cellTree/examples/go.results.to.latex.example.R
cellTree/inst
cellTree/inst/CITATION
cellTree/inst/doc
cellTree/inst/doc/cellTree-vignette.R
cellTree/inst/doc/cellTree-vignette.Rnw
cellTree/inst/doc/cellTree-vignette.pdf
cellTree/man
cellTree/man/HSMM_lda_model.Rd
cellTree/man/cell.ordering.table.Rd
cellTree/man/cellTree-package.Rd
cellTree/man/compute.backbone.tree.Rd
cellTree/man/compute.go.enrichment.Rd
cellTree/man/compute.lda.Rd
cellTree/man/ct.plot.go.dag.Rd
cellTree/man/ct.plot.grouping.Rd
cellTree/man/ct.plot.heatmap.Rd
cellTree/man/ct.plot.topics.Rd
cellTree/man/get.cell.dists.Rd
cellTree/man/go.results.to.latex.Rd
cellTree/vignettes
cellTree/vignettes/cellTree-vignette.Rnw