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    39 repositories

    • 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
      •206•939•7•1•Updated Apr 5, 2024Apr 5, 2024

    • transcriptionary

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 3, 2024Apr 3, 2024

    • bedder-rs

      Public
      an API for intersections of genomic data
      Rust
      •
      MIT License
      •0•74•4•0•Updated Apr 1, 2024Apr 1, 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

    • Snakemake_Tutorial

      Public
      tutorialpipelinejoshua
      Python
      •1•5•0•0•Updated Aug 14, 2023Aug 14, 2023

    • STRling

      Public
      Detect novel (and reference) STR expansions from short-read data
      strhacktoberfestwhole-genome-sequencingnim-langshort-tandem-repeats
      Nim
      •
      MIT License
      •9•61•21•1•Updated Aug 7, 2023Aug 7, 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
      •1•15•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.
      variantsscorevcfannopathogenic-variants
      Python
      •
      MIT License
      •8•21•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
      •2•3•1•0•Updated Feb 8, 2022Feb 8, 2022

    • sllobs-biostats

      Public
      HTML
      •18•70•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

    • smoove-nf

      Public
      Nextflow implementation of the smoove workflow and other tools for SV calling and QC
      Python
      •
      MIT License
      •2•0•0•0•Updated Nov 12, 2020Nov 12, 2020

    • kmertools

      Public
      Python
      •
      MIT License
      •1•3•0•0•Updated May 27, 2020May 27, 2020

    • ccrhtml

      Public
      A small repo for storing the code for making the files and html for CCRs.
      HTML
      •5•22•0•0•Updated Oct 22, 2019Oct 22, 2019

    • tmp

      Public
      A temporary repository to transfer issues
      0•0•0•0•Updated Oct 10, 2019Oct 10, 2019

    • ccr

      Public
      Building the constrained coding regions (CCR) model
      Python
      •
      MIT License
      •7•16•1•0•Updated Dec 19, 2018Dec 19, 2018

    • exacresiduals

      Public
      CCR model
      constraint
      Python
      •1•0•2•0•Updated Oct 2, 2018Oct 2, 2018