cellTree (version 1.2.2)

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

Description

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.

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Version

1.2.2

License

Artistic-2.0

Maintainer

David duVerle

Last Published

February 15th, 2017

Functions in cellTree (1.2.2)

cellTree-package

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

compute.lda

LDA model inference

go.results.to.latex

LaTeX output for Gene Ontology Enrichment results

ct.plot.heatmap

Gene Expression Heatmap

ct.plot.grouping

Plot cell tree with grouping information

cell.ordering.table

Ranking of cells according to backbone tree structure

ct.plot.topics

Plot cell tree with topic distributions

compute.go.enrichment

Gene Ontology enrichment analysis

ct.plot.go.dag

Gene Ontology enrichment sets plotting

HSMM_lda_model

Pre-computed LDA model for HSMMSingleCell data

compute.backbone.tree

Backbone Tree construction

get.cell.dists

Cell Pairwise-Distance Matrix