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    41 repositories

    • lr-annotation

      Public
      Tools for callset annotation in long-read cohorts.
      WDL
      •
      MIT License
      •0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • denovo-snv-indels

      Public
      Python
      •0•0•0•0•Updated Dec 17, 2025Dec 17, 2025

    • variant-interpretation

      Public
      WDL
      •7•5•0•1•Updated Dec 16, 2025Dec 16, 2025

    • annotations

      Public
      WDL
      •0•0•0•0•Updated Dec 15, 2025Dec 15, 2025

    • gatk-sv-internal

      Public
      Miscellaneous workflows and scripts for GATK-SV
      WDL
      •1•0•0•0•Updated Dec 9, 2025Dec 9, 2025

    • clinical-filtering

      Public
      Python
      •2•0•0•0•Updated Nov 7, 2025Nov 7, 2025

    • preprocessing

      Public
      WDL
      •0•0•0•0•Updated Oct 29, 2025Oct 29, 2025

    • XDP_postmortembrains

      Public
      Repository for preprocessing and analysis scripts for RNA-Seq data for the paper, "X-linked dystonia-parkinsonism is a genetic four-repeat tauopathy"
      R
      •0•0•0•0•Updated Sep 22, 2025Sep 22, 2025

    • XDP_ASO_2025

      Public
      Scripts and pipelines for XDP ASO study in NSCs using transcriptomics profiling
      R
      •0•0•0•0•Updated Sep 19, 2025Sep 19, 2025

    • gCNV-analysis-tools

      Public
      Analysis tools for gCNV
      R
      •1•0•3•0•Updated Sep 15, 2025Sep 15, 2025

    • outlier-exclusion

      Public
      Workflows for filtering gATK-SV callsets
      WDL
      •0•0•1•1•Updated Aug 9, 2025Aug 9, 2025

    • cadm2_recursive_splicing

      Public
      Analysis scripts used for the cadm2 recusirve splicing project including differential gene, de novo transcript reconstruction, transcript quantification plotting, and sawtooth pattern quantification.
      R
      •0•0•0•0•Updated Aug 5, 2025Aug 5, 2025

    • kj-variant-interpretation

      Public
      WDL
      •7•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • sva_typer

      Public
      A tool for genotyping SVA elements and substructure
      Rust
      •0•0•0•0•Updated Jun 30, 2025Jun 30, 2025

    • dsmap

      Public
      Shell
      •
      MIT License
      •1•0•2•0•Updated Mar 25, 2025Mar 25, 2025

    • athena

      Public
      Toolkit for structural variation mutation rates and dosage sensitivity
      Python
      •
      MIT License
      •0•0•2•0•Updated Feb 4, 2025Feb 4, 2025

    • cnv-validation

      Public
      WDL
      •1•0•0•1•Updated Oct 8, 2024Oct 8, 2024

    • SMC_CNN_Model

      Public
      Pipelines to reproduce analysis result for the SMC new target paper
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 23, 2024Jun 23, 2024

    • count_variant_occurrence

      Public
      WDL
      •
      MIT License
      •1•0•0•0•Updated Jun 17, 2024Jun 17, 2024

    • pzm

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 10, 2024Jun 10, 2024

    • 1kgp-gatk-sv-test

      Public
      Test GATK-SV on 1KGP Subset
      WDL
      •
      MIT License
      •0•0•0•0•Updated Apr 24, 2024Apr 24, 2024

    • gCNV-QC-Update

      Public
      Update to the gCNV QC step
      R
      •0•0•0•0•Updated Apr 4, 2024Apr 4, 2024

    • PlotCritic

      Public
      Python deployment tool for bespoke image curation projects, oriented toward scientific projects. Please cite https://academic.oup.com/gigascience/article/7/7/giy064/5026174
      Shell
      •
      MIT License
      •3•0•0•0•Updated Aug 17, 2023Aug 17, 2023

    • rWGCNA

      Public
      Resampled consensus WGCNA
      R
      •1•3•0•0•Updated May 4, 2023May 4, 2023

    • rCNV2

      Public
      Aggregation and analyses of rare CNVs across diseases
      R
      •
      MIT License
      •4•15•1•0•Updated Jan 25, 2023Jan 25, 2023

    • gnomad-sv-v3-qc

      Public
      Fork of GATK-SV repo from June 10, 2021, for gnomAD-SV v3 filtering, QC, and post-processing
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •76•0•0•0•Updated Oct 7, 2022Oct 7, 2022

    • TADA_2022

      Public
      R
      •5•2•1•0•Updated May 24, 2022May 24, 2022

    • svtk

      Public archive
      Python
      •12•35•18•0•Updated Mar 2, 2021Mar 2, 2021

    • gnomad-sv-pipeline

      Public archive
      Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)
      R
      •
      MIT License
      •14•37•3•0•Updated Jun 19, 2020Jun 19, 2020

    • gatk4-exome-analysis-pipeline

      Public
      This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •42•0•0•0•Updated Jan 13, 2020Jan 13, 2020