# Time course sequencing data analysis

## Documentation for package ‘TCseq’ version 1.0.0

- 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 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