GitHub - sgreenstein/pairwise-subspecific-origins: Compares the subspecific origins for all pairs of genome regions across multiple strains

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Compares the subspecific origins for all pairs of genome regions across multiple strains

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Name		Name	Last commit message	Last commit date
Latest commit History 60 Commits
.gitignore		.gitignore
LICENSE		LICENSE
NotInBackgroundApp.py		NotInBackgroundApp.py
OriginsAtPointPairApp.py		OriginsAtPointPairApp.py
README		README
SubspecificOriginsApp.py		SubspecificOriginsApp.py
TwoLocusWebHelper.py		TwoLocusWebHelper.py
UniqueCombinationsApp.py		UniqueCombinationsApp.py
dumpOrigins.py		dumpOrigins.py
pairwiseGenome.js		pairwiseGenome.js
pairwiseMarkers.py		pairwiseMarkers.py
sample_dict.p		sample_dict.p
strain_sets.json		strain_sets.json
subspecies.py		subspecies.py
subspeciesCython.pyx		subspeciesCython.pyx
test.csv		test.csv
test2.csv		test2.csv
twolocus.py		twolocus.py

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# pairwise-subspecies-origins

Tools for studying epistasis in the mouse genome.  More generally, given a set of genomes, each of which consists of labelled intervals, count the frequency of two-locus combinations.

The class `TwoLocus` implements the key functions.  To do run a test on a toy example, run `python twolocus.py`. This will compute incidence matrices from the labelled intervals in `test.csv`, then count and display the frequency of two-locus combinations.