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    21 repositories

    • msyd

      Public
      Python
      •
      MIT License
      •0•9•8•0•Updated Sep 27, 2024Sep 27, 2024

    • syri

      Public
      Synteny and Rearrangement Identifier
      Cython
      •
      MIT License
      •35•324•15•1•Updated Sep 9, 2024Sep 9, 2024

    • haplotype_threading

      Public
      Here are the scripts for pan-genome based haplotype threading with short reads (by Craig Dent)
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 30, 2024Aug 30, 2024

    • apricot_layer_mutations

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Aug 29, 2024Aug 29, 2024

    • snrna_eqtl_mapping

      Public
      Pipeline for processing 10X snRNAseq data to map eQTLs in recombinant gametes
      Jupyter Notebook
      •0•0•0•0•Updated Aug 2, 2024Aug 2, 2024

    • plotsr

      Public
      Tool to plot synteny and structural rearrangements between genomes
      Python
      •
      MIT License
      •28•279•6•0•Updated May 22, 2024May 22, 2024

    • chromodo

      Public
      Toolbox for genome assemblies and chromosomes
      MIT License
      •0•0•0•0•Updated May 17, 2024May 17, 2024

    • fixchr

      Public
      Python
      •
      MIT License
      •1•13•3•0•Updated Jan 18, 2024Jan 18, 2024

    • findGSE

      Public
      findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a skew normal distribution model.
      R
      •10•34•3•0•Updated Jan 16, 2024Jan 16, 2024

    • RTIGER

      Public
      R
      •4•0•0•0•Updated Jul 19, 2023Jul 19, 2023

    • DrLink

      Public
      Detecting recombination breakpoints using Linked read sequencing
      C++
      •3•3•0•0•Updated Jul 3, 2023Jul 3, 2023

    • GameteBinning_prac

      Public
      Here are the codes for a practice of gamete binning with simulated data
      C++
      •
      MIT License
      •0•3•0•0•Updated Feb 17, 2022Feb 17, 2022

    • toolbox

      Public
      Python
      •2•6•0•0•Updated Feb 14, 2022Feb 14, 2022

    • GameteBinning_tetraploid

      Public
      This is used to achieve haplotype-resolved assembly of tetraploid genomes using gamete sequencings
      C++
      •
      MIT License
      •1•11•0•0•Updated Oct 1, 2021Oct 1, 2021

    • AMPRIL-genomes

      Public
      scripts for the project of seven thaliana genomes assembly
      Python
      •18•36•9•0•Updated May 22, 2021May 22, 2021

    • GameteBinning

      Public
      C++
      •
      MIT License
      •3•12•2•0•Updated Nov 23, 2020Nov 23, 2020

    • AMPRIL-GI

      Public
      The scripts used in the project "The evolutionary dynamics of genetic incompatibilities introduced by duplicated genes in Arabidopsis thaliana"
      Perl
      •1•2•0•0•Updated Sep 3, 2020Sep 3, 2020

    • Hexaploid_MA_lines

      Public
      scripts pertaining to analysis of the hexaploid mutation accumulation lines
      Python
      •0•0•0•0•Updated Jun 9, 2020Jun 9, 2020

    • Scripts_supporting_Kiefer_Willing_et_al_2019

      Public
      Scripts_supporting_Kiefer_Willing_et_al_2019
      R
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Apr 23, 2019Apr 23, 2019

    • SHOREmap_v3.x

      Public
      C++
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Aug 22, 2018Aug 22, 2018

    • genomevar

      Public
      Identification of genomic differences from whole-genome alignments
      C++
      •2•4•0•0•Updated Aug 24, 2017Aug 24, 2017