Summary of available tools.

GAMtools provides a number of different utilities for working with GAM data. The table below summarizes the tools available in the suite.

Utility Description
call_windows Call positive windows for individual NPs
compaction Calculate chromatin compaction
convert Convert between different GAM matrix formats
enrichment Calculate enrichments of SLICE interactions
matrix Generate a GAM matrix from a segregation file
permute_segregation Circularly permute the columns of a GAM segregation file
plot_np Plot the segregation results for a particular NP
process_nps Map raw GAM sequencing data and call positive windows
radial_pos Calculate chromatin radial position
select Select only certain samples from a segregation file