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    35 repositories

    • Ctyper

      Public
      Genotyping of paralog specific gene types
      C++
      •
      MIT License
      •4•22•0•0•Updated Aug 28, 2026Aug 28, 2026

    • ctyper-kmc

      Public
      ctyper modified to read kmc input
      C++
      •0•0•0•0•Updated Jul 30, 2026Jul 30, 2026

    • hmcnc

      Public
      Hidden Markov Model based Copy number caller
      C++
      •1•20•0•0•Updated Jul 18, 2026Jul 18, 2026

    • CLASH

      Public
      Chromatin Loop Across-sample Score Harmonizer
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 27, 2026May 27, 2026

    • CARD-VNTR

      Public
      Tandem repeat analysis for the CARD consortium
      WDL
      •0•1•0•0•Updated May 25, 2026May 25, 2026

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •4.1k•0•0•0•Updated May 25, 2026May 25, 2026

    • vamos

      Public
      VNTR annotation using motif selection
      C
      •
      GNU General Public License v2.0
      •6•44•14•0•Updated May 25, 2026May 25, 2026

    • extend_ctyper_database

      Public
      Code to extend the ctyper database
      Python
      •0•0•0•0•Updated Feb 12, 2026Feb 12, 2026

    • SegDupAnnotation2

      Public
      Count gene duplications.
      Python
      •
      Other
      •1•2•0•0•Updated Dec 12, 2025Dec 12, 2025

    • chaissonlab.github.io

      Public
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Nov 27, 2025Nov 27, 2025

    • HelpHBAGenotyping

      Public
      Some utilities for ctyper/hba genotyping
      Python
      •1•1•0•1•Updated Nov 18, 2025Nov 18, 2025

    • spark-TR-analysis

      Public
      VNTR analysis of Spark autism data using danbing-tk + raava
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 20, 2025Aug 20, 2025

    • danbing-tk

      Public
      Toolkit for VNTR genotyping and repeat-pan genome graph construction
      tandem-repeatsgenome-graphgraph-aligner
      tandem-repeatsgenome-graphgraph-alignergenotypingvntr
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•36•10•1•Updated Aug 18, 2025Aug 18, 2025

    • aou_test

      Public
      testing for all of us
      C++
      •0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • ukb-danbing-raava

      Public
      danbing-tk + raava analysis pipeline for UK BioBank
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jun 25, 2025Jun 25, 2025

    • raava

      Public
      Rare tandem repeat variant detection
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 25, 2025Jun 25, 2025

    • countme

      Public
      Counts methylated CpG's in reads according to intervals in a bed file. Meant for inserted sequences.
      C++
      •0•0•0•0•Updated Jun 17, 2025Jun 17, 2025

    • rare-var-scratch

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • L1Scan

      Public
      Scan a bam file for l1 insertions.
      C++
      •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • SegDupAnnotation

      Public
      Python
      •2•9•1•0•Updated Sep 16, 2024Sep 16, 2024

    • devas

      Public
      Deep learning validation of SV calls
      Python
      •1•2•0•0•Updated Sep 12, 2024Sep 12, 2024

    • vamos-somatic

      Public
      A wdl file for generating per-read calls for tandem repeats in long-read data.
      WDL
      •0•0•0•0•Updated Jul 10, 2024Jul 10, 2024

    • GTEx-tools

      Public
      Small tool-list for gtex
      C++
      •0•0•0•0•Updated Jun 23, 2024Jun 23, 2024

    • RepeatMasking

      Public
      A snakefile to run repeatmasker on genomes in a scatter/gather approach.
      Python
      •2•0•1•0•Updated Feb 2, 2024Feb 2, 2024

    • LRA

      Public
      Long read aligner
      C++
      •
      Other
      •8•115•15•0•Updated May 26, 2023May 26, 2023

    • TT-Mars

      Public
      Structural Variants Assessment Based on Haplotype-resolved Assemblies
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•21•3•0•Updated Apr 28, 2023Apr 28, 2023

    • eMotif_manuscript_analysis_scripts

      Public
      Analysis scripts associated with the manuscript "The motif composition of variable-number tandem repeats impacts gene expression", including bias correction, eQ…
      Jupyter Notebook
      •0•1•2•0•Updated Mar 4, 2023Mar 4, 2023

    • mcst

      Public
      Simple sam manipulation code. Includes inversion finding.
      C++
      •0•0•0•0•Updated Dec 8, 2022Dec 8, 2022

    • sedef

      Public
      Identification of segmental duplications in the genome
      C++
      •
      MIT License
      •7•0•0•0•Updated Jun 11, 2021Jun 11, 2021

    • PartitionedAssembly

      Public
      Simple phase partitioned pipeline
      C++
      •1•0•0•0•Updated Jul 16, 2020Jul 16, 2020
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