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    23 repositories

    • xAIWorkshop

      Public
      A Repository of Notebooks, Revision notes and Presentation tools for the Explainable AI in Biology Conference in October 2024.
      TeX
      •2•5•0•0•Updated Oct 14, 2024Oct 14, 2024

    • GenCHORD

      Public
      A Bayesian method to smooth-out the noise in a coverage dataset, revealing the underlying average behaviour which is constrained to lie on `Harmonics' of a fundamental coverage value.
      C++
      •
      GNU General Public License v3.0
      •0•0•11•0•Updated Jul 15, 2024Jul 15, 2024

    • CoverageWorkshop

      Public
      A Workshop Notebook used for running a session as part of the OpenLab series.
      Jupyter Notebook
      •1•0•0•0•Updated Feb 12, 2024Feb 12, 2024

    • stepStone

      Public
      A pipeline for identification of chromothripsis breakpoints and cancer rearrangements
      C
      •
      MIT License
      •0•0•0•0•Updated Dec 22, 2023Dec 22, 2023

    • HypoCoverage

      Public
      Coverage Analysis Tools
      C++
      •0•0•0•0•Updated Jul 10, 2023Jul 10, 2023

    • MCSampler

      Public
      An MCMC Sampling framework for sampling from arbitrary probability densities.
      C++
      •0•0•0•0•Updated Jan 18, 2023Jan 18, 2023

    • scaffHiC

      Public
      Pipeline for genome scaffolding by modelling distributions of HiC pairs
      bioinformaticshic-analysishic-qcgenome-scaffolding
      C
      •
      MIT License
      •1•10•3•0•Updated Dec 7, 2022Dec 7, 2022

    • HypothesisTester

      Public
      A Bayesian Statistical Inference framework for comparing hypotheses
      C++
      •0•0•0•0•Updated Oct 18, 2022Oct 18, 2022

    • ContactPointAnalysis

      Public
      A statistical tool for analysing the Contact Point hypothesis for Chromothripsis
      C++
      •0•0•0•0•Updated Aug 26, 2022Aug 26, 2022

    • Scaff10X

      Public
      Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
      bioinformaticsgenomicsgenomeassemblyscaffoldingbreaking10xgenomics
      C
      •
      MIT License
      •3•21•24•3•Updated Aug 2, 2022Aug 2, 2022

    • chromoSPA

      Public
      A Size and Positional Analysis (SPA) tool for studying chromothripsis breakages.
      C++
      •
      MIT License
      •0•0•0•0•Updated Jun 28, 2022Jun 28, 2022

    • scaffhtag

      Public
      Pipeline for scaffolding genome assemblies using haplotagging reads
      C
      •
      MIT License
      •1•0•0•0•Updated May 17, 2022May 17, 2022

    • LinkStats

      Public
      Collect and process statistics from aligned linked-reads.
      C
      •
      Other
      •0•0•0•0•Updated Jan 17, 2022Jan 17, 2022

    • HiLine

      Public
      HiC alignment and classification pipeline
      Python
      •
      Other
      •0•4•1•0•Updated Oct 8, 2021Oct 8, 2021

    • SamHaplotag

      Public
      Process haplotag barcodes in SAM format
      C++
      •
      MIT License
      •1•2•0•0•Updated Jun 29, 2021Jun 29, 2021

    • caus

      Public
      CAUS is a pipeline for Chromosome Assignment Using Synteny
      C
      •
      MIT License
      •0•5•2•0•Updated May 17, 2021May 17, 2021

    • easyChain

      Public
      easyChain is a pipeline to produce a chain file from two genome assemblies.
      C
      •
      MIT License
      •1•4•0•0•Updated Mar 9, 2021Mar 9, 2021

    • covidPileup

      Public
      Pipeline for building SNP and GAP pileup from multiple COVID-19 whole genome sequences.
      C
      •
      MIT License
      •0•0•0•0•Updated Jun 30, 2020Jun 30, 2020

    • varibase

      Public
      A pipeline to correct variation errors of SNPs/indles from genome assembly
      C
      •
      MIT License
      •0•0•0•0•Updated May 4, 2020May 4, 2020

    • SIMDExtensionWrapper

      Public
      Generic wrapper program, detects SIMD CPU extensions and launches an appropriate sub-process.
      C
      •
      Other
      •1•1•0•0•Updated Nov 20, 2019Nov 20, 2019

    • AncesBin

      Public
      Pipeline to bin 10X, HiC, PacBio and ONT reads based on ancestry assemblies
      genome-assembly10xontgenome-ancestryreads-binningpacbiohic
      C
      •
      MIT License
      •0•1•0•0•Updated Oct 14, 2019Oct 14, 2019

    • scanPAV

      Public
      Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
      bioinformaticsgenomicsbioinformatics-pipelinestructurevariationgenomes-comparisongenome-mappingpipelinefastasmaltgenome-alignment
      C
      •
      MIT License
      •7•29•3•0•Updated Mar 5, 2018Mar 5, 2018

    • smis

      Public
      SMIS: Single Molecular Integrative Scaffolding. A pipeline for scaffolding genome assemblies using long reads (PacBio, ONT)
      genomeassemblypacbioscaffoldinglong-readsontoxfordnanopore
      C
      •
      GNU General Public License v3.0
      •2•4•2•0•Updated Feb 19, 2018Feb 19, 2018