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    45 repositories

    • tapestry

      Public
      Weaving DNA methylation data onto the genetic background of human pedigrees and trios
      Jupyter Notebook
      •0•0•0•0•Updated Jul 3, 2026Jul 3, 2026

    • CIDR_preprocessing

      Public
      Python
      •0•0•0•0•Updated Jun 9, 2026Jun 9, 2026

    • tapestry-tools

      Public
      Tools to process DNA methylation from HiFi reads that have been phased to the haplotypes of the pedigree's founders.
      Jupyter Notebook
      •0•0•0•0•Updated May 15, 2026May 15, 2026

    • bedder-rs

      Public
      an API for intersections of genomic data
      Rust
      •
      MIT License
      •4•148•5•1•Updated Mar 12, 2026Mar 12, 2026

    • HiFi-human-WGS-WDL

      Public
      Fork to remove tools we don't need
      WDL
      •
      BSD 3-Clause Clear License
      •56•1•0•0•Updated Jan 24, 2026Jan 24, 2026

    • wdl-common

      Public
      Fork to remove tools we don't need
      WDL
      •
      BSD 3-Clause Clear License
      •16•0•0•0•Updated Dec 22, 2025Dec 22, 2025

    • STRling

      Public
      Detect novel (and reference) STR expansions from short-read data
      strhacktoberfestwhole-genome-sequencing
      strhacktoberfestwhole-genome-sequencingnim-langshort-tandem-repeats
      Nim
      •
      MIT License
      •10•71•21•2•Updated Dec 6, 2025Dec 6, 2025

    • constraint-tools

      Public
      Tools to discover natural selection given multiple evolved DNA sequences (e.g., gnomad cohort, or multiple tumor samples)
      vuejsspavuex
      vuejsspavuexmap-reduceaxiosvue-materialsnvflask-apikmer-countingpysam
      Jupyter Notebook
      •
      MIT License
      •0•1•8•0•Updated Sep 11, 2025Sep 11, 2025

    • Snakemake_Tutorial

      Public
      tutorialpipelinejoshua
      tutorialpipelinejoshua
      Python
      •0•12•0•0•Updated Mar 25, 2025Mar 25, 2025

    • normo-vs-oligo-manuscript

      Public
      HTML
      •0•0•0•0•Updated Sep 13, 2024Sep 13, 2024

    • applied-computational-genomics

      Public
      Applied Computational Genomics Course at UU: Spring 2020
      HTML
      •
      Creative Commons Attribution Share Alike 4.0 International
      •239•1.1k•8•1•Updated Apr 5, 2024Apr 5, 2024

    • transcriptionary

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Apr 3, 2024Apr 3, 2024

    • proj-mutator-mapping

      Public
      Code for reproducing analysis and figures from https://elifesciences.org/reviewed-preprints/89096
      Python
      •
      MIT License
      •1•1•0•0•Updated Feb 23, 2024Feb 23, 2024

    • mutator-epistasis-manuscript

      Public
      HTML
      •
      Creative Commons Attribution 4.0 International
      •3•0•0•1•Updated Oct 25, 2023Oct 25, 2023

    • CEPH-K1463-TandemRepeats

      Public
      Jupyter Notebook
      •5•0•0•0•Updated Aug 1, 2023Aug 1, 2023

    • ceph-dnm-manuscript

      Public
      Code used for figure generation and statistical analysis for https://elifesciences.org/articles/46922
      Jupyter Notebook
      •
      MIT License
      •4•3•0•2•Updated Jul 6, 2023Jul 6, 2023

    • human-rae-manuscript

      Public
      code used for figure generation and statistical analysis for manuscript
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Dec 4, 2022Dec 4, 2022

    • 2022-10-11-Utah-Python

      Public
      HTML
      •
      Other
      •1•0•0•0•Updated Oct 11, 2022Oct 11, 2022

    • bedqc

      Public
      BED QC tool (in the making)
      HTML
      •
      MIT License
      •2•18•12•0•Updated Aug 19, 2022Aug 19, 2022

    • uu-delphi-datascience

      Public
      0•0•0•0•Updated Apr 25, 2022Apr 25, 2022

    • pathoscore

      Public
      pathoscore evaluates variant pathogenicity tools and scores.
      variantsscorevcfanno
      variantsscorevcfannopathogenic-variants
      Python
      •
      MIT License
      •8•22•3•2•Updated Mar 25, 2022Mar 25, 2022

    • covdist

      Public
      simple coverage profile of aligned samples. useful for sequencing center feedback and topoffs.
      HTML
      •
      MIT License
      •1•0•0•0•Updated Mar 2, 2022Mar 2, 2022

    • covviz

      Public
      Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
      HTML
      •
      MIT License
      •7•1•0•0•Updated Feb 17, 2022Feb 17, 2022

    • STRling-nf

      Public
      Nextflow implementation of STRling data flow
      Nextflow
      •
      MIT License
      •3•3•1•0•Updated Feb 8, 2022Feb 8, 2022

    • sllobs-biostats

      Public
      HTML
      •18•75•5•1•Updated Jan 27, 2022Jan 27, 2022

    • idplot

      Public
      compare sequences to a shared root reference sequence.
      HTML
      •
      MIT License
      •4•0•0•0•Updated Oct 19, 2021Oct 19, 2021

    • facets-nf

      Public
      nextflow implementation of the facets data flow.
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Oct 11, 2021Oct 11, 2021

    • preon

      Public
      Precision Oncology data workflow
      Nextflow
      •0•0•0•0•Updated May 19, 2021May 19, 2021

    • vcf2db

      Public
      create a gemini-compatible database from a VCF
      Python
      •
      MIT License
      •13•55•23•2•Updated Jan 5, 2021Jan 5, 2021

    • freebayes-nf

      Public
      a better freebayes-parallel
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Jan 5, 2021Jan 5, 2021
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