Repositories list

• vamos

  Public

  ChaissonLab/vamos’s past year of commit activity
  VNTR annotation using motif selection

  C

  •

  GNU General Public License v2.0

  •5•39•13•0•Updated Dec 18, 2025Dec 18, 2025

• SegDupAnnotation2

  Public

  ChaissonLab/SegDupAnnotation2’s past year of commit activity
  Count gene duplications.

  Python

  •

  Other

  •1•2•0•0•Updated Dec 12, 2025Dec 12, 2025

• hmcnc

  Public

  ChaissonLab/hmcnc’s past year of commit activity
  Hidden Markov Model based Copy number caller

  C++

  •1•20•0•0•Updated Dec 9, 2025Dec 9, 2025

• chaissonlab.github.io

  Public

  ChaissonLab/chaissonlab.github.io’s past year of commit activity
  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

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.7k•0•0•0•Updated Nov 17, 2025Nov 17, 2025

• Ctyper

  Public

  ChaissonLab/Ctyper’s past year of commit activity
  Genotyping of paralog specific gene types

  C++

  •

  MIT License

  •3•17•0•0•Updated Nov 6, 2025Nov 6, 2025

• CARD-VNTR

  Public
  Tandem repeat analysis for the CARD consortium

  WDL

  •0•1•0•0•Updated Sep 8, 2025Sep 8, 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

  ChaissonLab/danbing-tk’s past year of commit activity
  Toolkit for VNTR genotyping and repeat-pan genome graph construction

  tandem-repeatsgenome-graphgraph-aligner+ 2genotypingvntr

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •5•31•8•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•14•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, eQTL mapping, fine-mapping, and genome folding prediction.

  Jupyter Notebook

  •0•0•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

• danbing-tk_rxiv

  Public archive
  Genome-wide genotyping of VNTRs from short-read datasets with haplotype-resolved database

  C++

  •0•0•0•0•Updated Jul 15, 2020Jul 15, 2020

• AssemblyAnalysis

  Public
  Python

  •0•0•0•1•Updated Jun 11, 2020Jun 11, 2020

• GenomeIndex

  Public
  paths to genome data -> download

  0•0•0•0•Updated Jun 10, 2019Jun 10, 2019