Time course sequencing data analysis

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Documentation for package ‘TCseq’ version 1.11.0

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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 binding analysis
DBresult This function performs differetial analysis by fitting read Perform likelihood ratio tests and extract the differential analysis results
DBresult.cluster This function performs differetial analysis by fitting read Perform likelihood ratio tests and extract the differential analysis results
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