Repositories list

• the-blood-virome

  Public
  Corresponding code for the NAO's blog post titled, "Exploring Blood-Based Biosurveillance, Part 3: The Blood Virome"

  JavaScript

  •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

• mgs-workflow

  Public
  Nextflow

  •

  MIT License

  •2•4•43•5•Updated Jan 31, 2025Jan 31, 2025

• basecall

  Public
  Python

  •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

• p2ra-manuscript

  Public
  Python

  •0•0•8•0•Updated Jan 25, 2025Jan 25, 2025

• ont-analysis

  Public
  Scripts with which to analyze ONT sequencing results

  Python

  •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• basecall-workflow

  Public
  Nextflow workflow to run basecalling on Nanopore data

  Nextflow

  •0•0•3•0•Updated Jan 23, 2025Jan 23, 2025

• simons-notebook

  Public
  HTML

  •1•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• simon-analysis

  Public
  One-off scripts

  Jupyter Notebook

  •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• tagging-test

  Public
  MWE for testing Nextflow tagging behavior

  Nextflow

  •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

• mgs-uci-data-paper

  Public
  R

  •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

• mgs-pipeline

  Public
  Python

  •

  MIT License

  •1•3•1•0•Updated Nov 27, 2024Nov 27, 2024

• scenario-simulator

  Public
  HTML

  •

  MIT License

  •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

• wills-public-notebook

  Public
  Public notebook for Will's analyses.

  HTML

  •0•0•0•0•Updated Oct 18, 2024Oct 18, 2024

• harmons-public-notebook

  Public
  JavaScript

  •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

• air-mgs-analysis

  Public
  Shell

  •0•0•0•0•Updated Oct 13, 2024Oct 13, 2024

• jefftk-analysis

  Public
  A repo for checking in one-off analysis scripts

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

• air-sampling-figure

  Public
  Data and code to recreate Figure 1 from "Indoor Air Sampling for Detection of Viral Nucleic Acids"

  Python

  •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

• p2ra

  Public
  Python

  •1•4•6•2•Updated Aug 15, 2024Aug 15, 2024

• krona-compare

  Public
  Python

  •

  MIT License

  •0•1•0•0•Updated Jul 20, 2024Jul 20, 2024

• mgs-workflow-core

  Public
  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Jun 12, 2024Jun 12, 2024

• dans-notebook

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jun 7, 2024Jun 7, 2024

• rpkg-naoutils

  Public
  naoutils: An R package with helper functions for the NAO team

  R

  •

  Other

  •0•0•4•0•Updated May 22, 2024May 22, 2024

• phagemid-tracers

  Public
  HTML

  •1•0•0•0•Updated Dec 23, 2023Dec 23, 2023

• phagemid-decay-experiment

  Public
  R

  •0•1•0•0•Updated Dec 8, 2023Dec 8, 2023

• mikes-notebook

  Public
  Mike's notes and demo analyses

  HTML

  •0•0•0•0•Updated Sep 11, 2023Sep 11, 2023

• mag

  Public
  Assembly and binning of metagenomes

  Nextflow

  •

  MIT License

  •116•1•0•0•Updated Jul 20, 2023Jul 20, 2023

• frequent_flyers

  Public
  Modelling work performed for the NAO in February 2023

  Jupyter Notebook

  •1•0•0•0•Updated Jun 9, 2023Jun 9, 2023

• illumina_pilot

  Public
  HTML

  •0•1•0•0•Updated Mar 21, 2023Mar 21, 2023

• phagemid_amplicon_analyses

  Public
  HTML

  •0•1•0•0•Updated Mar 18, 2023Mar 18, 2023

• kmer-egd

  Public
  C++

  •

  MIT License

  •0•3•0•0•Updated Feb 13, 2023Feb 13, 2023