Creating BED tracks of TSSs and clusters of TSSs
CAGE data based expression clustering
Extracting tag clusters (TCs) for individual CAGE experiment from CAGEset object
Extracting consensus clusters from CAGEset object
Aggregating tag clusters across multiple CAGE datasets
Selecting consensus clusters with shifting score above specified threshold
Example CAGEset object with zebrafish CAGE data
Extracting elements of the specified expression class
Creating bedGraph/bigWig tracks of CAGE transcription starts sites
Importing publicly available CAGE data from various resources
Methods for function show
Calculating promoter shifting score
Extracting type of input files from CAGEset object
Setting colors for samples
Extracting CAGE datasets labels from CAGEset object
cumulativeCTSSdistribution
Calculating cumulative sum of CAGE signal along genomic region
Determining positions of CAGE signal quantiles within genomic region
Clustering CTSSs into tag clusters (TCs)
Extracting consensus clusters tpm matrix from CAGEset object
Reading CAGE data from input file(s) and detecting TSSs
Extracting labels of expression classes
Extracting paths to input files from CAGEset object
Merging CAGE datasets (samples)
Class "CAGEset"
Extracting CTSS clustering method from CAGEset object
Plotting expression profiles derived from CAGE data
Plotting reverse cumulative number of CAGE tags per CTSS
Plotting pairwise scatter plots of CAGE signal and calculating correlation between samples
Extracting normalized CAGE signal for TSSs from CAGEset object
List of FANTOM5 human CAGE samples
Extracting genomic coordinates of TSSs from CAGEset object
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Extracting CAGE tag count for TSSs from CAGEset object
List of FANTOM5 mouse CAGE samples
Normalizing raw CAGE tag count
Merging two CAGEset objects into one
Extracting genome name from CAGEset object
Extracting library sizes from CAGEset object
Plotting distribution of interquantile width