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1. mapLoopLoci mapLoopLoci Public

   Maps loop loci from ChIA-pet/Hi-C/etc. experiments across samples, which may be different species and/or cell types. Uses the bnMapper algorithm for cross-species mappings.

   Python 4

2. mapGL mapGL Public

   Phylogenetic mapping of DNA element gain and loss using multiple outgroup species.

   Python 3 5

3. repeatMaskerUtils repeatMaskerUtils Public

   Utilities for working with RepeatMasker Libraries and Annotations.

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4. score_motifs score_motifs Public

   Calculate log-odds scores for transcription factor binding motifs.

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5. MapGL_analysis MapGL_analysis Public

   Scripts and data sources to reproduce results presented in "MapGL: Inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony." Diehl AG, and Boyle AP…

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6. ENCODEdBTools ENCODEdBTools Public

   Tools for getting data from the ENCODE portal API

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