TSS sequencing data analysis

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Documentation for package ‘TSSr’ version 0.99.21

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

annotateCluster	Annotate clusters with GFF annotation file.
annotateCluster-method	Annotate clusters with GFF annotation file.
assignedClusters	Access data stored in a TSSr object
assignedClusters-method	Access data stored in a TSSr object
callEnhancer	Identification of enhancers
callEnhancer-method	Identification of enhancers
clusterShape	Access data stored in a TSSr object
clusterShape-method	Access data stored in a TSSr object
clusterTSS	Cluster TSSs into tag clusters
clusterTSS-method	Cluster TSSs into tag clusters
consensusCluster	Make consensus clusters across multiple samples.
consensusCluster-method	Make consensus clusters across multiple samples.
consensusClusters	Access data stored in a TSSr object
consensusClusters-method	Access data stored in a TSSr object
deGene	Analysis of gene differential expression.
deGene-method	Analysis of gene differential expression.
DEtables	Access data stored in a TSSr object
DEtables-method	Access data stored in a TSSr object
enhancers	Access data stored in a TSSr object
enhancers-method	Access data stored in a TSSr object
exampleTSSr	TSSr example data
exportClustersTable	Export cluster tables
exportClustersTable-method	Export cluster tables
exportClustersToBed	Creating bed files of clusters
exportClustersToBed-method	Creating bed files of clusters
exportDETable	Export gene differential expression results table
exportDETable-method	Export gene differential expression results table
exportEnhancerTable	Export enhancer tables
exportEnhancerTable-method	Export enhancer tables
exportShapeTable	Export core promoter shape score tables
exportShapeTable-method	Export core promoter shape score tables
exportShiftTable	Export core promoter shift table
exportShiftTable-method	Export core promoter shift table
exportTSStable	Export TSS tables
exportTSStable-method	Export TSS tables
exportTSStoBedgraph	Creating Bedgraph/BigWig tracks of TSSs
exportTSStoBedgraph-method	Creating Bedgraph/BigWig tracks of TSSs
filteredClusters	Access data stored in a TSSr object
filteredClusters-method	Access data stored in a TSSr object
filterTSS	Filter raw TSS counts or normalized TSS
filterTSS-method	Filter raw TSS counts or normalized TSS
getTSS	Precisely identify TSSs from bam files, paired end bam files, bed files, BigWig files, tss files, or tss tables.
getTSS-method	Precisely identify TSSs from bam files, paired end bam files, bed files, BigWig files, tss files, or tss tables.
librarySizes	Access data stored in a TSSr object
librarySizes-method	Access data stored in a TSSr object
mergeSamples	Merge TSS samples
mergeSamples-method	Merge TSS samples
normalizeTSS	Normalize raw TSS counts
normalizeTSS-method	Normalize raw TSS counts
plotCorrelation	Pairwise scatter plots and correlations of TSS signal
plotCorrelation-method	Pairwise scatter plots and correlations of TSS signal
plotDE	Plot gene differential expressions
plotDE-method	Plot gene differential expressions
plotInterQuantile	Plot core promoter interquantile width
plotInterQuantile-method	Plot core promoter interquantile width
plotShape	Plot core promoter shape
plotShape-method	Plot core promoter shape
plotTSS	Plot TSSs and clusters
plotTSS-method	Plot TSSs and clusters
plotTssPCA	Plotting principle component analysis (PCA)
plotTssPCA-method	Plotting principle component analysis (PCA)
PromoterShift	Access data stored in a TSSr object
PromoterShift-method	Access data stored in a TSSr object
refTable	Access data stored in a TSSr object
refTable-method	Access data stored in a TSSr object
shapeCluster	Analysis of core promoter shape
shapeCluster-method	Analysis of core promoter shape
shiftPromoter	Select genes which have core promoter shift across different experiments.
shiftPromoter-method	Select genes which have core promoter shift across different experiments.
show-method	Display a compact summary of a TSSr object
tagClusters	Access data stored in a TSSr object
tagClusters-method	Access data stored in a TSSr object
TAGtables	Access data stored in a TSSr object
TAGtables-method	Access data stored in a TSSr object
TSSmatrix	Access data stored in a TSSr object
TSSmatrix-method	Access data stored in a TSSr object
TSSr	TSSr: A package for transcription start site sequencing data analyses.
TSSr-accessors	Access data stored in a TSSr object
TSSr-class	TSSr: A package for transcription start site sequencing data analyses.
unassignedClusters	Access data stored in a TSSr object
unassignedClusters-method	Access data stored in a TSSr object