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    25 repositories

    • clique

      Public
      Read alignment and collapsing for lineage data
      Rust
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Aug 8, 2026Aug 8, 2026

    • FlashFry

      Public
      FlashFry: The rapid CRISPR target site characterization tool
      bioinformaticscrisprcrispr-cas9
      bioinformaticscrisprcrispr-cas9genome-editing
      Scala
      •
      Other
      •13•83•3•0•Updated Jul 27, 2026Jul 27, 2026

    • REMAP_Analysis_Pipeline

      Public
      Analysis pipeline for MARC1 mouse barcode system
      Python
      •0•0•0•0•Updated Jun 11, 2026Jun 11, 2026

    • PALINCODE

      Public
      a place to store code for the palindrome base-editing effort
      Jupyter Notebook
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • AML_lineage_tracing

      Public
      AML lineage tracing effort
      R
      •
      MIT License
      •0•0•0•0•Updated Mar 29, 2026Mar 29, 2026

    • gene_146

      Public
      Code and course material for Gene/QBS 146: Foundations of Bioinformatics I
      Jupyter Notebook
      •2•4•0•0•Updated Feb 23, 2026Feb 23, 2026

    • counterfeiter

      Public
      simulated lineage trees with cell patterning options
      Rust
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 15, 2025Dec 15, 2025

    • ruststarcode

      Public
      a partial reimplementation of the starcode approach to barcode collapsing
      Rust
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 24, 2025Oct 24, 2025

    • butcher

      Public
      A opinionated read trimmer
      Rust
      •0•0•0•0•Updated Oct 13, 2023Oct 13, 2023

    • Circuitseq

      Public
      Nanopore Plasmid Sequencing
      JavaScript
      •
      Other
      •2•34•6•0•Updated Oct 10, 2023Oct 10, 2023

    • PhysiCell-Studio-2.26.122

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 8, 2023Aug 8, 2023

    • TreeUtils

      Public
      A simple Scala tool to handle running the PHILIP MIX parsimony program and generating JSON output trees
      Scala
      •
      GNU General Public License v3.0
      •0•7•0•0•Updated May 8, 2023May 8, 2023

    • NextLineage

      Public
      Lineage recorder processing using NextFlow
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 27, 2023Jan 27, 2023

    • PennGrader

      Public
      A seamless in-line Jupyter Notebook autograder.
      Python
      •11•0•0•0•Updated Dec 30, 2022Dec 30, 2022

    • DupScoop

      Public
      Remove duplicate segments from small, circular genome assemblies
      Rust
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 1, 2022Dec 1, 2022

    • editing_plots

      Public
      split out the editing plots to refactor them
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Oct 26, 2022Oct 26, 2022

    • gene111

      Public
      Notebooks and code for Dartmouth's GENE111 class
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •6•2•0•0•Updated Jun 13, 2021Jun 13, 2021

    • mckennalab.github.io

      Public
      the rendered version of the website
      HTML
      •0•1•0•0•Updated May 25, 2021May 25, 2021

    • SingleCellLineage

      Public archive
      Updated scripts and pipelines for processing GESTALT data at single-cell resolution
      Scala
      •10•20•1•0•Updated May 22, 2021May 22, 2021

    • SAMToFasta

      Public
      Convert a SAM and reference files into a paired FASTA alignment file
      Rust
      •
      GNU General Public License v3.0
      •0•2•3•0•Updated Oct 28, 2020Oct 28, 2020

    • COVID_scheduler

      Public archive
      auto-schedule people for COVID lab access
      Python
      •0•0•0•0•Updated Jul 12, 2020Jul 12, 2020

    • hugo_academic_website

      Public
      the templated version of the website
      TeX
      •
      MIT License
      •1•0•0•0•Updated Jul 1, 2020Jul 1, 2020

    • SciMaul

      Public archive
      SCIMaul: A read splitter for single-cell experiments
      Scala
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Apr 10, 2019Apr 10, 2019

    • custom_barcodes

      Public archive
      Generation of custom sequencing barcodes
      Scala
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•2•0•0•Updated Nov 12, 2018Nov 12, 2018

    • SC_GESTALT

      Public
      GESTALT processing pipeline for barcodes captured with single-cell RNA sequencing
      Scala
      •6•0•0•0•Updated Dec 30, 2017Dec 30, 2017
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