Repositories list

• marc_infra

  Public
  Shell

  •0•0•0•0•Updated Jan 5, 2026Jan 5, 2026

• marc_web

  Public
  A web interface for querying mARC

  HTML

  •1•0•0•0•Updated Jan 5, 2026Jan 5, 2026

• marc_db

  Public
  Python

  •0•0•0•0•Updated Dec 17, 2025Dec 17, 2025

• SampleRegistry

  Public
  Web application to keep track of samples sequenced

  Python

  •3•0•7•4•Updated Dec 15, 2025Dec 15, 2025

• marc_honest

  Public
  Honest broker for mARC db

  Python

  •0•0•0•4•Updated Dec 15, 2025Dec 15, 2025

• 16S_QIIME2

  Public template
  Snakemake based 16S QIIME2 pipeline

  Python

  •7•1•0•2•Updated Dec 9, 2025Dec 9, 2025

• CHOP_metadata_checker

  Public
  HTML

  •3•0•11•0•Updated Dec 5, 2025Dec 5, 2025

• unassigner

  Public
  Type strain identification for 16S reads

  Python

  •5•5•8•3•Updated Nov 24, 2025Nov 24, 2025

• dnabc

  Public
  Identify DNA barcodes in high-throughput sequencing data files

  Python

  •

  GNU General Public License v2.0

  •6•0•0•3•Updated Nov 24, 2025Nov 24, 2025

• seqBackup

  Public
  Python

  •5•1•1•3•Updated Nov 18, 2025Nov 18, 2025

• heyfastq

  Public
  FASTQ utilities in pure python with no dependencies

  Jupyter Notebook

  •1•0•0•2•Updated Oct 23, 2025Oct 23, 2025

• cost_estimator

  Public
  An internal utility for keeping track of price estimates

  0•0•0•0•Updated Apr 28, 2025Apr 28, 2025

• adonisplus

  Public
  R

  •

  GNU General Public License v3.0

  •2•3•1•0•Updated Nov 23, 2024Nov 23, 2024

• PCMP_ITS_pipeline

  Public
  R

  •1•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• PennChopMicrobiomeProgram.github.io

  Public
  Dev board for PCMP

  SCSS

  •0•0•0•0•Updated Oct 23, 2024Oct 23, 2024

• mirix

  Public
  Quantify the susceptibility of a bacterial community to an antibiotic.

  R

  •1•3•1•1•Updated Jul 18, 2024Jul 18, 2024

• whatbacteria

  Public
  Database of bacterial phenotypes and antibiotic susceptibility

  R

  •0•0•0•0•Updated Jun 26, 2024Jun 26, 2024

• wfrcwf

  Public
  Python

  •0•0•0•0•Updated Jun 18, 2024Jun 18, 2024

• primertrim

  Public
  Trim primers from reads

  Python

  •1•1•0•1•Updated Jun 5, 2024Jun 5, 2024

• TagSequencingPipeline

  Public archive
  Shell

  •5•0•3•2•Updated May 2, 2024May 2, 2024

• ZIBR

  Public
  Zero-Inflated Beta Random Effect model

  R

  •

  Other

  •10•31•0•0•Updated Oct 17, 2023Oct 17, 2023

• microflowseq

  Public
  R

  •

  Other

  •0•0•1•1•Updated Aug 31, 2023Aug 31, 2023

• bacphene

  Public
  Imports Bacterial Phenotype Data Into R

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 20, 2023Mar 20, 2023

• gutsandcages

  Public
  A package to calculate power for mouse and rat experimental design

  R

  •

  Other

  •0•0•0•0•Updated Feb 18, 2022Feb 18, 2022

• ZIR

  Public
  Zero-Inflated (Wilcoxon and Kruskal–Wallis) Rank Test

  R

  •

  MIT License

  •4•12•4•0•Updated Oct 13, 2021Oct 13, 2021

• Rout_Tanes_SIV_ART_microbiome

  Public archive
  R

  •0•0•0•0•Updated Jul 30, 2021Jul 30, 2021

• ITS_PIPITS_BROCC

  Public archive
  R

  •2•0•0•0•Updated Apr 30, 2021Apr 30, 2021

• FARMM

  Public archive
  Code used to generate the results and figures for the FARMM study.

  1•0•0•0•Updated Jul 22, 2020Jul 22, 2020

• PathwayAbundanceFinder

  Public archive
  A short wrapper for finding presence/absence/abundance of pathways from metagenomic data.

  Python

  •4•0•3•1•Updated Jul 16, 2019Jul 16, 2019

• decontam

  Public archive
  Python

  •7•1•2•1•Updated Jan 19, 2018Jan 19, 2018