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    29 repositories

    • fugue

      Public
      FUGUE is a preprocessing tool for ALLEGRO
      Jupyter Notebook
      •1•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • allegro

      Public
      ALLEGRO: An Algorithm Leveraging Linear Programing to Enhance Guide RNA Optimization
      synthetic-biologylinear-programmingcombinatorial-optimizationcrispr-cas9genome-editingcrispr-design
      C++
      •
      MIT License
      •1•1•0•0•Updated Nov 12, 2024Nov 12, 2024

    • rambler

      Public
      Python
      •0•0•1•0•Updated Sep 10, 2024Sep 10, 2024

    • MSTmap

      Public
      A software tool that builds genetic linkage maps efficiently and accurately
      C++
      •
      Apache License 2.0
      •0•5•0•0•Updated Sep 8, 2024Sep 8, 2024

    • MSTmap-Python

      Public
      A Python wrapper for UCRBioInfo MSTmap
      C++
      •
      Apache License 2.0
      •1•0•0•0•Updated Sep 8, 2024Sep 8, 2024

    • deepguide_reborn

      Public
      A reimplementation of the original https://github.com/dDipankar/DeepGuide by Dipankar Ranjan Baisya
      Python
      •0•0•0•0•Updated May 6, 2024May 6, 2024

    • dmc_prediction

      Public
      Python
      •0•0•0•0•Updated Feb 20, 2024Feb 20, 2024

    • fosinopril

      Public
      Software for "In Vitro Antibabesial Activity of the ACE Inhibitor Fosinopril Requires Drug Activation by a Parasite Esterase BdFE1 "
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 21, 2023Aug 21, 2023

    • AMPS

      Public
      Python
      •0•1•0•0•Updated Apr 5, 2023Apr 5, 2023

    • GeneLocalizationBduncani

      Public
      Python
      •0•0•0•0•Updated May 17, 2022May 17, 2022

    • DeepGuide

      Public
      0•0•0•0•Updated Jan 24, 2022Jan 24, 2022

    • PGV

      Public
      Reference-agnostic Representation and Visualization of Pan-genomes
      Python
      •
      MIT License
      •3•18•3•0•Updated Sep 16, 2021Sep 16, 2021

    • MergeMap

      Public
      MergeMap is a software tool that builds accurate consensus genetic maps from a set of individual genetic maps
      C++
      •
      MIT License
      •0•2•0•0•Updated Jun 7, 2021Jun 7, 2021

    • cowpea_pangenome

      Public
      Companion website to cowpea pangenome paper
      Shell
      •0•0•0•0•Updated Mar 18, 2021Mar 18, 2021

    • DeeplyEssential

      Public
      Deep neural network based prediction model for gene essentiality prediction in microbes
      Python
      •1•10•1•0•Updated Feb 11, 2021Feb 11, 2021

    • SELFISH

      Public
      Selfish: Discovery of Differential Chromatin Interactions via a Self-Similarity Measure
      MATLAB
      •1•4•2•0•Updated Nov 18, 2019Nov 18, 2019

    • Epi2En

      Public
      Python
      •0•0•0•0•Updated Nov 4, 2019Nov 4, 2019

    • Novo_Stitch

      Public
      Novo&Stitch is a genome assembly reconciliation tool based on optical map.
      Python
      •1•10•0•0•Updated Oct 21, 2019Oct 21, 2019

    • DeepHistone

      Public
      Python
      •0•0•0•0•Updated Feb 2, 2019Feb 2, 2019

    • OMGS

      Public
      OMGS is a fast and accurate genome scaffolding tool with one or multiple Bionano optical maps
      Python
      •1•7•3•0•Updated Nov 4, 2018Nov 4, 2018

    • Chimericognizer

      Public
      Chimericognizer is a novel and accurate chimeric contigs correction tool based on optical maps.
      Python
      •1•8•1•0•Updated Jun 10, 2018Jun 10, 2018

    • XMView

      Public
      A Multiple Alignment XMap Viewer with Genetic Map Integration
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 15, 2018Jan 15, 2018

    • EAST

      Public
      EAST: Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps
      Python
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Oct 11, 2017Oct 11, 2017

    • ThIEF

      Public
      Finding Genome-wide Trajectories of Epigenetics Marks
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 27, 2017Jan 27, 2017

    • FMTP

      Public
      Fingerprint-based Minimal Tiling Path
      C++
      •0•0•0•0•Updated Aug 7, 2016Aug 7, 2016

    • BRAT_nova

      Public
      Fast and accurate mapping of bisulfite-treated reads
      C++
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2016Aug 1, 2016

    • PuFFIN

      Public
      A Parameter-free Method to Build Genome-wide Nucleosome Maps from Paired-end Sequencing Data
      Python
      •
      MIT License
      •1•1•0•0•Updated Jul 30, 2016Jul 30, 2016

    • NOrMAL

      Public
      Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model
      C++
      •
      MIT License
      •0•0•0•0•Updated Jul 28, 2016Jul 28, 2016

    • LRTag

      Public
      LRTag is a tool that is capable of efficiently selecting a near optimal set of SNP markers across multiple populations.
      C++
      •
      MIT License
      •0•0•0•0•Updated Jul 28, 2016Jul 28, 2016