Code

We believe in making our code open source. The following GitHub repositories contain genomics tools you may find useful:

  • seqr is a software tool we use for searching for causal variants in Mendelian disease families.
  • LOFTEE is a plugin for the Ensembl Variant Effect Predictor that improves the detection and filtering of candidate protein-truncating variants.
  • exac_browser is the code behind our ExAC browser.
  • clinvar provides tools to parse NCBI’s ClinVar database, and a flat file representation thereof.
  • gene_lists is a collection of gene lists for genome-wide analyses.
  • minimal_representation is a collection of scripts for canonicalizing the representation of genomic variants.
  • denovolyzeR is an R package for testing the gene-wise burden of de novo variants in disease families compared to random mutational expectations.
  • igv_plotter automates the generation of IGV screenshots for sequencing reads at variant sites of interest.
  • matchbox is a software application that serves as our primary bridge to the MatchMaker Exchange.
  • gnomad_browser is derived from the ExAC browser and is the code that powers our gnomAD browser.

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