Time course sequencing data analysis

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Documentation for package ‘TCseq’ version 1.33.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

clust	clust class
clust-class	clust class
clust.accessors	Accessors to extract slots of a clust class.
clustCenters	Accessors to extract slots of a clust class.
clustCenters-method	Accessors to extract slots of a clust class.
clustCluster	Accessors to extract slots of a clust class.
clustCluster-method	Accessors to extract slots of a clust class.
clustData	Accessors to extract slots of a clust class.
clustData-method	Accessors to extract slots of a clust class.
clustMembership	Accessors to extract slots of a clust class.
clustMembership-method	Accessors to extract slots of a clust class.
clustResults	Accessors to extract slots of a TCA class.
clustResults-method	Accessors to extract slots of a TCA class.
countReads	count mapped reads overlap genomic intervals
counts	Extracts counts of a TCA object.
counts-method	Extracts counts of a TCA object.
counts<--method	Extracts counts of a TCA object.
countsTable	An example read Counts table
DBanalysis	Perform differential expression analysis
DBresult	This function tests for differential expression
DBresult.cluster	This function tests for differential expression
design	Accessors to extract slots of a TCA class.
design-method	Accessors to extract slots of a TCA class.
experiment	An example experiment design without BAM file infomration
experiment_BAMfile	An example experiment design with BAM file infomration
genomicFeature	Accessors to extract slots of a TCA class.
genomicFeature-method	Accessors to extract slots of a TCA class.
genomicIntervals	An example reference genomic regions
peakreference	combine and merge multiple BED files
TCA	TCA class and constructor
TCA-class	TCA class and constructor
TCA.accessors	Accessors to extract slots of a TCA class.
TCAFromSummarizedExperiment	TCA class and constructor
tca_ATAC	An example TCA object
tcTable	Accessors to extract slots of a TCA class.
tcTable-method	Accessors to extract slots of a TCA class.
timeclust	time couse data clustering
timeclustplot	Plot clustering results for time course data.
timecourseTable	constructs time course table for clustering analysis