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TSSr-class
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TSSr: A package for transcription start site sequencing data analyses. |
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TSSr-package
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TSSr: A package for transcription start site sequencing data analyses. |
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annotateCluster()
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Annotate clusters with GFF annotation file. |
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clusterTSS()
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Cluster TSSs into tag clusters |
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consensusCluster()
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Make consensus clusters across multiple samples. |
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deGene()
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Analysis of gene differential expression. |
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exampleTSSr exampleTSSr
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TSSr example data |
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exportClustersTable()
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Export cluster tables |
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exportClustersToBed()
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Creating bed files of clusters |
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exportDETable()
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Export gene differential expression results table |
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exportShapeTable()
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Export core promoter shape score tables |
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exportShiftTable()
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Export core promoter shift table |
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exportTSStable()
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Export TSS tables |
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exportTSStoBedgraph()
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Creating Bedgraph/BigWig tracks of TSSs |
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filterTSS()
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Filter raw TSS counts or normalized TSS |
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getTSS()
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Precisely identify TSSs from bam files, paired end bam files, bed files, BigWig files, tss files, or tss tables. |
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mergeSamples()
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Merge TSS samples |
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normalizeTSS()
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Normalize raw TSS counts |
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plotCorrelation()
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Pairwise scatter plots and correlations of TSS signal |
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plotDE()
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Plot gene differential expressions |
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plotInterQuantile()
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Plot core promoter interquantile width |
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plotShape()
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Plot core promoter shape |
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plotTSS()
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Plot TSSs and clusters |
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plotTssPCA()
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Plotting principle component analysis (PCA) |
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shapeCluster()
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Analysis of core promoter shape |
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shiftPromoter()
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Select genes which have core promoter shift across different experiments. |