Repositories list

• 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

• damlab-wrappers

  Public
  A collection of Snakemake wrappers and multiqc plugins targeted at Nanopore HIV sequence analysis.

  Python

  •0•0•0•0•Updated May 19, 2025May 19, 2025

• quantitative-reasoning-in-biology

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Mar 11, 2025Mar 11, 2025

• cigarmath

  Public
  A collection of python utilities for manipulating CIGARS.

  Python

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 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

  •33•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

  •21•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

  •367•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

  •11•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

  •164•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

  •97•0•0•0•Updated Sep 15, 2020Sep 15, 2020

• HIV-nanopore-pipeline

  Public
  HIV-specific nanopore sequencing pipeline

  Python

  •0•1•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

• RPI-DL-Architecture-Review

  Public
  Holds all models, weights, scripts, etc. used to compare RPI DL architectures

  Jupyter Notebook

  •0•0•0•0•Updated Jul 5, 2020Jul 5, 2020

• nanopore-analysis

  Public
  Basic Nanopore Snakemakes for Nanopore analysis

  Shell

  •0•0•0•0•Updated Jun 29, 2020Jun 29, 2020

• DeepLabCut

  Public
  Markerless pose estimation of user-defined features with deep learning for all animals, including humans

  Python

  •

  GNU Lesser General Public License v3.0

  •1.7k•0•0•0•Updated Jan 8, 2020Jan 8, 2020

• Genomic-ULMFiT

  Public
  ULMFiT for Genomic Sequence Data

  Jupyter Notebook

  •55•0•0•0•Updated Nov 15, 2019Nov 15, 2019

• chroCRISPR

  Public
  Analysis scripts for Molecular Therapy paper

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Oct 24, 2019Oct 24, 2019