Overview¶
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 |