Man pages for Linlab-slu/TSSr
TSS sequencing data analysis

annotateClusterAnnotate clusters with GFF annotation file.
clusterTSSCluster TSSs into tag clusters
consensusClusterMake consensus clusters across multiple samples.
deGeneAnalysis of gene differential expression.
exampleTSSrTSSr example data
exportClustersTableExport cluster tables
exportClustersToBedCreating bed files of clusters
exportDETableExport gene differential expression results table
exportShapeTableExport core promoter shape score tables
exportShiftTableExport core promoter shift table
exportTSStableExport TSS tables
exportTSStoBedgraphCreating Bedgraph/BigWig tracks of TSSs
filterTSSFilter raw TSS counts or normalized TSS
getTSSPrecisely identify TSSs from bam files, paired end bam files,...
mergeSamplesMerge TSS samples
normalizeTSSNormalize raw TSS counts
plotCorrelationPairwise scatter plots and correlations of TSS signal
plotDEPlot gene differential expressions
plotInterQuantilePlot core promoter interquantile width
plotShapePlot core promoter shape
plotTSSPlot TSSs and clusters
plotTssPCAPlotting principle component analysis (PCA)
shapeClusterAnalysis of core promoter shape
shiftPromoterSelect genes which have core promoter shift across different...
TSSr-classTSSr: A package for transcription start site sequencing data...
TSSr-packageTSSr: A package for transcription start site sequencing data...
Linlab-slu/TSSr documentation built on July 28, 2021, 12:59 a.m.