R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 12 found.
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HSMM_lda_model (Package: cellTree) : Pre-computed LDA model for HSMMSingleCell data

Pre-computed LDA model for HSMMSingleCell data

● Data Source: BioConductor
● Keywords: data
● Alias: HSMM_lda_model
● 0 images

cell.ordering.table (Package: cellTree) : Ranking of cells according to backbone tree structure

Produces a table of input cells ranked by their position in the backbone tree.

● Data Source: BioConductor
● Keywords:
● Alias: cell.ordering.table
● 0 images

cellTree-package (Package: cellTree) : Inference and visualisation of Single-Cell RNA-seq Data data as a hierarchical tree structure

This packages computes a Latent Dirichlet Allocation (LDA) model of single-cell RNA-seq data and build a compact tree modelling the relationship between individual cells over time or space.

● Data Source: BioConductor
● Keywords:
● Alias: cellTree, cellTree-package
● 0 images

compute.backbone.tree (Package: cellTree) : Backbone Tree construction

Builds a ‘backbone tree’ from a fitted LDA model.

● Data Source: BioConductor
● Keywords:
● Alias: compute.backbone.tree
● 1 images

compute.go.enrichment (Package: cellTree) : Gene Ontology enrichment analysis

Computes enrichment scores for Gene Ontology terms associated with genes in each topic.

● Data Source: BioConductor
● Keywords:
● Alias: compute.go.enrichment
● 0 images

compute.lda (Package: cellTree) : LDA model inference

This function fits a Latent Dirichlet Allocation (LDA) to single-cell RNA-seq data.

● Data Source: BioConductor
● Keywords:
● Alias: compute.lda
● 0 images

ct.plot.go.dag (Package: cellTree) : Gene Ontology enrichment sets plotting

Plots DAG of significantly enriched terms for all topics, along with ancestor nodes.

● Data Source: BioConductor
● Keywords:
● Alias: ct.plot.go.dag
● 1 images

ct.plot.grouping (Package: cellTree) : Plot cell tree with grouping information

Plots a backbone tree (or MST) that was computed with compute.backbone.tree, displaying each cell's grouping.

● Data Source: BioConductor
● Keywords:
● Alias: ct.plot.grouping
● 1 images

ct.plot.heatmap (Package: cellTree) : Gene Expression Heatmap

Plots a heatmap of gene expression, with cells ordered according to the structure computed by compute.backbone.tree.

● Data Source: BioConductor
● Keywords:
● Alias: ct.plot.heatmap
● 0 images

ct.plot.topics (Package: cellTree) : Plot cell tree with topic distributions

Plots a backbone tree (or MST) that was computed with compute.backbone.tree, displaying each cell's topic distribution as a pie chart.

● Data Source: BioConductor
● Keywords:
● Alias: ct.plot.topics
● 1 images