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    42 repositories

    • NanoPal-Snakemake

      Public
      A Snakemake version of https://github.com/WeichenZhou/NanoPal-and-Cas9-targeted-enrichment-pipelines
      Shell
      •0•1•0•0•Updated May 4, 2026May 4, 2026

    • Boyle-Lab.github.io

      Public
      HTML
      •0•0•0•0•Updated Apr 29, 2026Apr 29, 2026

    • minimera

      Public
      Tool to detect foldback chimeras in Oxford Nanopore data using minimizers.
      Common Lisp
      •
      Other
      •0•0•0•0•Updated Apr 10, 2026Apr 10, 2026

    • F-Seq2

      Public
      Improving the feature density based peak caller with dynamic statistics
      dnase-seqchip-seqpeak-caller
      dnase-seqchip-seqpeak-calleratac-seqkernel-density-estimationidridr-analysis
      Python
      •
      GNU General Public License v3.0
      •1•7•3•4•Updated Feb 3, 2026Feb 3, 2026

    • HaplotagLR

      Public
      A tool for phasing long-read sequencing results.
      Python
      •
      MIT License
      •1•6•3•0•Updated Aug 19, 2025Aug 19, 2025

    • 5-RACE

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Jul 28, 2025Jul 28, 2025

    • GPatch-Manuscript

      Public
      Data retrieval and Analysis steps for the GPatch manuscript.
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 24, 2025Jun 24, 2025

    • nanopore_guide_design

      Public
      Nextflow pipeline for generating, filtering, and prioritizing candidate guide RNA sequences
      Python
      •0•1•0•0•Updated Apr 7, 2025Apr 7, 2025

    • SEMpl

      Public
      C++ implementation of the SEM algorithm
      bioinformatics
      bioinformatics
      C
      •3•16•0•0•Updated Dec 18, 2024Dec 18, 2024

    • HMMSTR

      Public
      Python
      •
      MIT License
      •4•14•1•0•Updated Dec 16, 2024Dec 16, 2024

    • OnRamp-Web-App

      Public
      JavaScript
      •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • HMMSTR_depreciated

      Public
      Python
      •
      MIT License
      •4•4•0•1•Updated Sep 12, 2024Sep 12, 2024

    • NanoPal-and-Cas9-targeted-enrichment-pipelines

      Public
      The pipelines for the project 'Cas9 targeted enrichment of mobile elements using nanopore sequencing', including NanoPal and Cleavage-site analysis
      Shell
      •3•1•0•0•Updated Aug 22, 2023Aug 22, 2023

    • TRACE

      Public
      TRACE: HMM for DNase footprinting and motif matching
      C
      •
      GNU General Public License v3.0
      •7•7•6•0•Updated Jun 1, 2023Jun 1, 2023

    • bulkPlasmidSeq

      Public
      Python
      •2•2•0•0•Updated Jan 17, 2023Jan 17, 2023

    • CGIMP

      Public
      Clustered Genomic Interval Mapping Platform
      JavaScript
      •
      GNU General Public License v3.0
      •2•1•0•1•Updated Aug 9, 2022Aug 9, 2022

    • MergeBW

      Public
      Tool for merging many BigWig files for RegulomeDB
      C++
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Apr 4, 2022Apr 4, 2022

    • read-based-TE-Enrichment

      Public
      Repeat enrichment testing for short-read sequencing data using an assembly-free alignment approach.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 12, 2021Oct 12, 2021

    • TRACE_GPU

      Public
      Accelerate TRACE algorithm with GPU computing
      C
      •0•0•0•0•Updated Sep 21, 2021Sep 21, 2021

    • RegulomeDB-TURF

      Public
      Data repository for TURF paper
      Jupyter Notebook
      •0•3•2•0•Updated Sep 21, 2021Sep 21, 2021

    • TE-Driven-CTCF-Loop-Evol

      Public
      R
      •3•9•0•0•Updated Jun 29, 2021Jun 29, 2021

    • SEMplMe

      Public
      Implementation of the SEM algorithm with incorporation of DNA methylation
      C
      •1•1•0•0•Updated Jun 3, 2021Jun 3, 2021

    • Blacklist

      Public
      Application for making ENCODE Blacklists
      bioinformatics
      bioinformatics
      C++
      •
      GNU General Public License v3.0
      •42•337•11•0•Updated Apr 23, 2021Apr 23, 2021

    • short-read-seq_snakemake

      Public
      SnakeMake pipeline for alignment, filtering, and peak-calling for short-read sequencing data.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 1, 2021Mar 1, 2021

    • ATACseq-Snakemake

      Public
      Standard Parker Lab ATAC-seq processing pipeline in Snakemake form
      Python
      •4•0•0•0•Updated Nov 20, 2020Nov 20, 2020

    • F-Seq2-Paper-Supplementary

      Public
      F-Seq2 paper data accession numbers and scripts to run peak callers.
      Python
      •1•0•0•0•Updated Sep 30, 2020Sep 30, 2020

    • mapGL

      Public
      Phylogenetic mapping of DNA element gain and loss using multiple outgroup species.
      Python
      •
      MIT License
      •5•0•0•0•Updated Jul 15, 2020Jul 15, 2020

    • UNCALLED

      Public
      Raw nanopore signal mapper that enables real-time targeted sequencing
      C++
      •
      MIT License
      •44•0•0•0•Updated Mar 3, 2020Mar 3, 2020

    • pyblast

      Public
      Run NCBI BLAST with an easy-to-use Pythonic wrapper
      Python
      •
      MIT License
      •6•0•0•0•Updated Dec 27, 2019Dec 27, 2019

    • Porechop

      Public
      adapter trimmer for Oxford Nanopore reads
      C++
      •
      GNU General Public License v3.0
      •137•0•0•0•Updated Aug 30, 2019Aug 30, 2019
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