One-Step to Cluster and Visualize Gene Expression Data

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Documentation for package ‘ClusterGVis’ version 0.1.2

• DESCRIPTION file.

Help Pages

BEAM_res	This is a test data for this package test data describtion
clusterData	Cluster Data Based on Different Methods
enrichCluster	Perform GO/KEGG Enrichment Analysis for Multiple Clusters
exprs	Generic to access cds count matrix
exprs-method	Method to access cds count matrix
exps	This is a test data for this package test data describtion
filter.std	using filter.std to filter low expression genes
filter.std modified by Mfuzz filter.std	using filter.std to filter low expression genes
getClusters	Determine Optimal Clusters for Gene Expression or Pseudotime Data
net	This is a test data for this package test data describtion
normalized_counts	Return a size-factor normalized and (optionally) log-transformed expression
plot_genes_branched_heatmap2	Create a heatmap to demonstrate the bifurcation of gene expression along two branchs which is slightly modified in monocle2
plot_multiple_branches_heatmap2	Create a heatmap to demonstrate the bifurcation of gene expression along multiple branches
plot_pseudotime_heatmap2	Plots a pseudotime-ordered, row-centered heatmap which is slightly modified in monocle2
prepareDataFromscRNA	Prepare scRNA Data for clusterGvis Analysis
pre_pseudotime_matrix	Calculate and return a smoothed pseudotime matrix for the given gene list
pseudotime	Generic to extract pseudotime from CDS object
pseudotime-method	Method to extract pseudotime from CDS object
sig_gene_names	This is a test data for this package test data describtion
size_factors	Get the size factors from a cds object.
termanno	This is a test data for this package test data describtion
termanno2	This is a test data for this package test data describtion
traverseTree	traverseTree function
visCluster	using visCluster to visualize cluster results from clusterData and enrichCluster output