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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.

    Perl 1

  4. score_motifs score_motifs Public

    Calculate log-odds scores for transcription factor binding motifs.

    Perl 1

  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

    Perl