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    51 repositories

    • cigarmath

      Public
      A collection of python utilities for manipulating CIGARS.
      Python
      •
      MIT License
      •0•0•0•0•Updated May 22, 2026May 22, 2026

    • spatial-tk

      Public
      A command-line toolkit for spatial transcriptomics data analysis
      Jupyter Notebook
      •2•0•0•1•Updated Apr 29, 2026Apr 29, 2026

    • damlab-wrappers

      Public
      A collection of Snakemake wrappers and multiqc plugins targeted at Nanopore HIV sequence analysis.
      Python
      •1•1•0•0•Updated Apr 13, 2026Apr 13, 2026

    • quantitative-reasoning-in-biology

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Apr 5, 2026Apr 5, 2026

    • damlab-skills

      Public
      A set of AgentSkills for bioinformatics analysis.
      Python
      •
      MIT License
      •1•0•0•2•Updated Apr 2, 2026Apr 2, 2026

    • BioinfoMCP

      Public
      HTML
      •
      MIT License
      •6•0•0•0•Updated Mar 12, 2026Mar 12, 2026

    • outerspace

      Public
      A python tool for extracting short sequences from NGS data with fuzzy regular expressions.
      Python
      •2•2•1•1•Updated Jan 20, 2026Jan 20, 2026

    • applied-biostats-helper

      Public
      A small collection of utilities to help with the Drexel MIIM-517 Applied Biostats class
      Python
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • collins-hiv-brainspleen

      Public
      The analysis code for HIV Brain/Spleen nanopore IPDA analysis
      0•0•0•0•Updated May 28, 2025May 28, 2025

    • nanopore-ipda

      Public
      A snakemake pipleline that implements an in-silico HIV Intact Proviral DNA Assay
      MIT License
      •0•0•0•0•Updated May 28, 2025May 28, 2025

    • siv-barcode-pipeline

      Public
      Python
      •0•0•0•0•Updated May 19, 2025May 19, 2025

    • VILOCA

      Public
      VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 13, 2025Jan 13, 2025

    • ice

      Public
      Synthego ICE - Inference of CRISPR Editing software
      Python
      •
      Other
      •34•0•0•0•Updated Jan 10, 2025Jan 10, 2025

    • OMICS

      Public
      Repo for students of the Advanced OMICS Course
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •18•13•0•0•Updated Dec 19, 2024Dec 19, 2024

    • pod5-file-format

      Public
      Pod5: a high performance file format for nanopore reads.
      C++
      •
      Other
      •38•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • Cas_HIV_hits

      Public
      Scripts and figures for Frontiers Manuscript.
      Jupyter Notebook
      •0•0•0•0•Updated Nov 27, 2023Nov 27, 2023

    • the-littlest-jupyterhub

      Public
      Simple JupyterHub distribution for 1-100 users on a single server
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •373•1•0•0•Updated Sep 2, 2022Sep 2, 2022

    • HIV-Quasipore-basecallers

      Public
      Other
      •0•6•0•0•Updated Jun 5, 2022Jun 5, 2022

    • snakedeploy

      Public
      deploy a snakemake pipeline directly from version control (under development)
      Python
      •
      Mozilla Public License 2.0
      •13•1•0•0•Updated May 18, 2022May 18, 2022

    • hiv-transformers

      Public
      A collection of Hugging Face tools for analyzing HIV
      Jupyter Notebook
      •0•2•0•0•Updated Apr 11, 2022Apr 11, 2022

    • Neurocog_Tat-miRNA_binding_analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 28, 2021Aug 28, 2021

    • DL_RPI_prediton_benchmak

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 28, 2021Aug 28, 2021

    • SAE-based_RPI_negative_sample_generation

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 28, 2021Aug 28, 2021

    • pbmeth

      Public
      PacBio CpG Methylation prediction using Fast.ai
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 18, 2021Feb 18, 2021

    • artic-ncov2019

      Public
      ARTIC nanopore protocol for nCoV2019 novel coronavirus
      Python
      •
      Creative Commons Attribution 4.0 International
      •162•0•0•0•Updated Feb 18, 2021Feb 18, 2021

    • pipeline-multitool

      Public
      Python
      •0•0•0•0•Updated Nov 3, 2020Nov 3, 2020

    • nbdev_template

      Public template
      Template for nbdev projects
      Jupyter Notebook
      •
      Apache License 2.0
      •96•0•0•0•Updated Sep 15, 2020Sep 15, 2020

    • HIV-nanopore-pipeline

      Public
      HIV-specific nanopore sequencing pipeline
      Python
      •0•2•0•0•Updated Sep 2, 2020Sep 2, 2020

    • htguideseq

      Public
      High Throughput GuideSeq Analysis
      Dockerfile
      •0•1•0•0•Updated Sep 1, 2020Sep 1, 2020

    • HIV-subtype-gRNAs

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 5, 2020Jul 5, 2020
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