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    11 repositories

    • REforge

      Public
      Regulatory Element Forward Genomics to associate transcription factor binding site divergence in regulatory elements with phenotypic differences between species
      Python
      •
      MIT License
      •3•8•6•1•Updated Oct 12, 2024Oct 12, 2024

    • TFforge

      Public
      Identifying transcription factors involved in phenotypic differences between species
      Python
      •
      MIT License
      •3•1•3•1•Updated Oct 12, 2024Oct 12, 2024

    • make_lastz_chains

      Public
      Portable solution to generate genome alignment chains using lastz
      bioinformaticsgenomicsbioinformatics-pipeline
      Python
      •
      MIT License
      •8•47•27•0•Updated Oct 11, 2024Oct 11, 2024

    • TOGA

      Public
      TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.
      bioinformaticsgenomicsbioinformatics-pipelinegenome-annotation
      Python
      •
      MIT License
      •23•156•29•1•Updated Jun 20, 2024Jun 20, 2024

    • GenomeAlignmentTools

      Public
      Tools for improving the sensitivity and specificity of genome alignments
      C
      •
      MIT License
      •15•56•14•0•Updated Jan 17, 2024Jan 17, 2024

    • IterativeErrorCorrection

      Public
      Iterative error correction of long reads
      Python
      •
      MIT License
      •3•11•4•1•Updated Dec 9, 2022Dec 9, 2022

    • CESAR2.0

      Public
      C
      •
      MIT License
      •10•28•7•0•Updated Dec 1, 2022Dec 1, 2022

    • GeneLossPipe

      Public
      Perl
      •
      MIT License
      •7•23•2•0•Updated Nov 29, 2022Nov 29, 2022

    • ForwardGenomics

      Public
      Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework
      Perl
      •
      MIT License
      •9•21•7•0•Updated Nov 29, 2022Nov 29, 2022

    • Parasol_LSF_Slurm

      Public
      A parasol-like wrapper around LSF or Slurm for efficiently handling batches of jobs on a compute cluster
      Perl
      •
      MIT License
      •2•2•4•0•Updated Jan 14, 2021Jan 14, 2021

    • CESAR

      Public
      Coding Exon Structure Aware Realigner
      Python
      •
      MIT License
      •1•5•0•1•Updated Mar 30, 2017Mar 30, 2017