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    16 repositories

    • SuRE-paper-codes

      Public
      Codes for the SuRE MPRA paper
      0•0•0•0•Updated Oct 12, 2026Oct 12, 2026

    • SuRE-sequence-processes

      Public
      Python
      •0•0•0•0•Updated Oct 11, 2026Oct 11, 2026

    • EvaReg-analysis

      Public
      All codes related to analysis of EvaReg models
      Jupyter Notebook
      •0•0•0•0•Updated Oct 11, 2026Oct 11, 2026

    • nSPECTRa

      Public
      Nextflow workflow to compute the mutation spectra
      Nextflow
      •
      MIT License
      •0•5•0•1•Updated Sep 22, 2026Sep 22, 2026

    • nf-LO

      Public
      A Nextflow workflow to generate lift over files for any pair of genomes
      bioinformaticsgenomeliftover
      bioinformaticsgenomeliftovernextflow-workflownextflow-dsl2
      Nextflow
      •
      MIT License
      •12•76•0•1•Updated Aug 26, 2026Aug 26, 2026

    • SuRE-gg-variants

      Public
      Genome graph-based analysis of regulatory variants in SuRE MPRA data
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 23, 2026Jun 23, 2026

    • bovreg-twas-suite

      Public
      bovreg-twas-suite is a modular Nextflow pipeline suite for performing transcriptome-wide association studies (TWAS) in cattle. It includes workflows to generate…
      Nextflow
      •
      Other
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • EvaReg-training

      Public
      Training code for EvaReg models
      Python
      •0•0•0•0•Updated Apr 9, 2026Apr 9, 2026

    • nf-VarAnno

      Public
      A cross-species variant annotation pipeline based on Nextflow
      Python
      •1•1•0•0•Updated Mar 18, 2025Mar 18, 2025

    • CattleGraphGenomePaper

      Public
      Set of script for the paper on the cattle graph genome
      Shell
      •1•14•0•0•Updated Jan 10, 2023Jan 10, 2023

    • GCRF_tutorial

      Public
      Material for the bioinformatics tutorial held in Tanzania in May 2022
      HTML
      •0•0•0•0•Updated May 24, 2022May 24, 2022

    • CattleOManalyses

      Public
      Script and some results from the Optical mapping SV analyses
      Shell
      •
      MIT License
      •0•1•0•0•Updated May 2, 2022May 2, 2022

    • wBuffaloVsCow

      Public
      Code accompanying manuscript "Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication"
      R
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Aug 21, 2020Aug 21, 2020

    • hapbin

      Public
      Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)
      C++
      •
      GNU General Public License v3.0
      •19•45•16•2•Updated Oct 24, 2019Oct 24, 2019

    • hapbinX

      Public
      Pairwise version of hapbin (https://github.com/evotools/hapbin) for studying the strength of selection on multi-allelic haplotypes
      C++
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 23, 2017Jun 23, 2017

    • mm-iHS

      Public
      Scripts for calculating mm-iHS
      Perl
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 16, 2016May 16, 2016
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