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    43 repositories

    • g4Discovery

      Public
      Pipeline for annotating/predicting G-Quadruplexes (G4s) in a genome sequence, combining pqsfinder and G4Hunter.
      bioinformaticspipelinegenomicsdna-sequencesg-quadruplexesg4hunterpqsfinder
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 25, 2025Jun 25, 2025

    • mapsea

      Public
      Mapping And Prediction of Shared Elements in Alignments
      bioinformaticspipelinegenomealignmentcomparative-genomicsg-quadruplexest2tevolutionary-genomics
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 16, 2025Jun 16, 2025

    • GreatApeT2T-G4s

      Public
      Evolutionary Dynamics of Predicted G-Quadruplexes in Human and Other Great Apes
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jun 16, 2025Jun 16, 2025

    • T2T_primate_nonB

      Public
      Shell
      •
      MIT License
      •2•0•0•0•Updated Mar 20, 2025Mar 20, 2025

    • AmpliCoNE-tool

      Public
      AmpliCoNE: Ampliconic Copy Number Estimator
      Python
      •0•1•0•0•Updated Dec 12, 2024Dec 12, 2024

    • human_mtDNA_duplexSeq

      Public
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Dec 5, 2024Dec 5, 2024

    • T2T_primate_autosomes

      Public
      Code from the Makova lab for the T2T primates autosome paper.
      Python
      •0•0•0•0•Updated Aug 5, 2024Aug 5, 2024

    • T2T_primate_XY

      Public
      Python
      •
      MIT License
      •0•12•1•0•Updated Jun 7, 2024Jun 7, 2024

    • mitonuclear_expression

      Public
      This is a repository for the article "Exploring the effects of mitonuclear interactions on mitochondrial DNA gene expression in humans" (doi: 10.3389/fgene.2022.797129).
      Jupyter Notebook
      •0•1•0•0•Updated Apr 11, 2024Apr 11, 2024

    • YAG_analysis

      Public
      Analysis scripts for "Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome in Great Apes"
      Raku
      •1•0•0•0•Updated Jul 31, 2023Jul 31, 2023

    • NoiseCancellingRepeatFinder

      Public
      Noise-Cancelling Repeat Finder
      Python
      •
      MIT License
      •5•25•6•0•Updated Apr 11, 2023Apr 11, 2023

    • nonB-Seq-Errors

      Public
      0•0•0•0•Updated Mar 24, 2023Mar 24, 2023

    • HalfDeep

      Public
      Automated detection of intervals covered at half depth by sequenced reads.
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•0•0•Updated Jan 21, 2023Jan 21, 2023

    • ChildhoodObesity_SIBSIGHT-Epigenetics

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 8, 2022Sep 8, 2022

    • overlaps

      Public
      Jupyter Notebook
      •0•5•0•0•Updated Mar 2, 2022Mar 2, 2022

    • nick-bfx

      Public
      Central repository for generally useful scripts
      bioinformaticsutilitiesgenomics
      Python
      •2•0•0•0•Updated Mar 2, 2022Mar 2, 2022

    • macaque-duplexSeq

      Public
      HTML
      •0•1•0•0•Updated Jan 3, 2022Jan 3, 2022

    • G4_Selection

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 5, 2021May 5, 2021

    • nonB-RegVar

      Public
      This repository contains all the computational tools used in our manuscript "Non-B DNA: The major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome".
      Jupyter Notebook
      •0•1•2•0•Updated Apr 3, 2021Apr 3, 2021

    • g4sscs

      Public
      Python
      •0•0•0•0•Updated Mar 10, 2021Mar 10, 2021

    • kalign-dunovo

      Public
      An adaptation of the Kalign multiple sequence aligner for use in the Du Novo pipeline.
      C
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Oct 29, 2020Oct 29, 2020

    • RecoverY

      Public
      K-mer based read classification for Y-chromosome specific sequencing and assembly
      Python
      •
      MIT License
      •5•10•1•0•Updated Sep 30, 2020Sep 30, 2020

    • great-ape-Y-evolution

      Public
      Python
      •5•2•0•0•Updated Sep 21, 2020Sep 21, 2020

    • L1_Project

      Public
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Jul 13, 2020Jul 13, 2020

    • Y-AmpGene_CN_GE_GreatApes

      Public
      Ampliconic genes on the great ape Y chromosomes
      R
      •0•0•0•0•Updated May 26, 2020May 26, 2020

    • mouse-duplexSeq

      Public
      0•0•0•0•Updated May 5, 2020May 5, 2020

    • DiscoverY

      Public
      K-mer based classifier for Y-contig identification from Whole Genome Assemblies
      Jupyter Notebook
      •
      MIT License
      •6•11•12•0•Updated Feb 19, 2020Feb 19, 2020

    • cluster-monitor

      Public
      View the status of the slurm cluster via a web interface.
      JavaScript
      •0•3•0•0•Updated Feb 17, 2020Feb 17, 2020

    • heterochromatin

      Public
      High inter- and intraspecific turnover of satellite repeats in great apes
      Python
      •1•0•0•0•Updated Jun 20, 2019Jun 20, 2019

    • GTEx_Testis_Analysis

      Public
      This repository contains scripts used for the analysis of 170 whole genome and testis RNAseq data set.
      R
      •0•0•0•0•Updated Apr 26, 2019Apr 26, 2019
    0