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Table 1 Segtools analysis commands (segtools-...)

From: Exploratory analysis of genomic segmentations with Segtools

Command Input Output Visualization
length-distribution S Segment length distribution by label violin, bar plots (Figure 2)
nucleotide-frequency S, G Mono-/dinucleotide frequency by label heat map (Figure IB)
signal-distribution S, G Signal mean and variance by label heat map (Figure 3)
transition S Transition frequency between labels heat map, graph diagram
aggregation S, A Label density around annotations line plot (Figure 1A)
compare S, S Edit distances among all pairs of labels heat map
overlap S, A Overlap of annotations by segments PR curve, heat map
preprocess A An annotation in binary format
flatten S, A Segmentation with a label for every combination of labels in the input segmentations
feature-distance S, A Distance from each segment to nearest feature
html-report S HTML summary of Segtools command outputs
  1. The commands offered by the Segtools package and their associated inputs and outputs. The first four commands analyze a single segmentation. The following three commands compare a segmentation to another segmentation or to an annotation. The last four commands generate no visualizations and are utilities to be used in conjunction with the other Segtools commands. In each row of the table, the second column indicates the input file types ("S" for segmentation, "A" for annotation, "G" for genomedata), and the fourth column indicates how the outputs are visualized (and a reference to an example figure in this article if one exists). "PR curve" refers to a precision-recall curve.