arcfish.tl

Chromatin Loops

General testing classes

tl.LoopTestAbstract	Abstract class for each test alternative.
tl.TwoSampleT	Test 3D distance by two sample T-test.
tl.AxisWiseF	Perform axis-wise F-test and combine p-values by aggregated Cauchy test.

Loop caller class

tl.LoopCaller

Class for chromatin loop calling.

Differential loop

tl.DiffLoop

Differential analysis of chromatin loops.

Other functions

tl.overlap	Given two list of intervals, for each interval in the first list, check if it overlaps with any interval from the second list.
tl.signal_overlap	For each locus in test_df, return 1 if the locus is also present in true_df; return 0 if the locus is not present in true_df.
tl.loop_overlap	For each locus pair (row) in test_df, return 3 if the locus air also presents in true_df (pair presents -> both loci overlapped); return 1 if one of the two loci presents in true_df; and return 2 if both loci present but they never present in the same row of true_df.
tl.all_possible_pairs

TADs and Compartments

TAD caller

tl.TADCaller

TAD calling class.

Differential TADs

tl.DiffRegion

Differential analysis of chromatin TADs.

A/B compartment caller

tl.ABCaller

Call A/B compartments from multiplexed imaging data using PCA.