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 |