Skip to content

@PennChopMicrobiomeProgram PennChopMicrobiomeProgram

Change the repository type filter

All

    Repositories list

    33 repositories

    • marc_web

      Public
      A web interface for querying mARC
      HTML
      •2•0•0•7•Updated Apr 27, 2026Apr 27, 2026

    • unassigner

      Public
      Type strain identification for 16S reads
      Python
      •5•5•8•2•Updated Apr 23, 2026Apr 23, 2026

    • heyfastq

      Public
      FASTQ utilities in pure python with no dependencies
      Jupyter Notebook
      •1•0•5•3•Updated Apr 16, 2026Apr 16, 2026

    • CHOP_metadata_checker

      Public
      HTML
      •3•0•11•8•Updated Apr 13, 2026Apr 13, 2026

    • SampleRegistry

      Public
      Web application to keep track of samples sequenced
      Python
      •3•0•7•0•Updated Apr 13, 2026Apr 13, 2026

    • primertrim

      Public
      Trim primers from reads
      Python
      •1•1•0•1•Updated Apr 8, 2026Apr 8, 2026

    • dnabc

      Public
      Identify DNA barcodes in high-throughput sequencing data files
      Python
      •
      GNU General Public License v2.0
      •6•0•0•5•Updated Apr 8, 2026Apr 8, 2026

    • adonisplus

      Public
      R
      •
      GNU General Public License v3.0
      •2•3•1•0•Updated Apr 6, 2026Apr 6, 2026

    • wfrcwf

      Public
      Python
      •0•0•0•0•Updated Apr 3, 2026Apr 3, 2026

    • whatbacteria

      Public
      Database of bacterial phenotypes and antibiotic susceptibility
      R
      •0•0•0•0•Updated Apr 2, 2026Apr 2, 2026

    • ZIR

      Public
      Zero-Inflated (Wilcoxon and Kruskal–Wallis) Rank Test
      R
      •
      MIT License
      •4•12•4•0•Updated Mar 6, 2026Mar 6, 2026

    • ZIBR

      Public
      Zero-Inflated Beta Random Effect model
      R
      •
      Other
      •10•31•0•0•Updated Mar 6, 2026Mar 6, 2026

    • mirix

      Public
      Quantify the susceptibility of a bacterial community to an antibiotic.
      R
      •1•3•0•0•Updated Mar 6, 2026Mar 6, 2026

    • marc_infra

      Public
      Shell
      •1•0•0•0•Updated Feb 5, 2026Feb 5, 2026

    • marc_db

      Public
      Python
      •0•0•0•0•Updated Jan 31, 2026Jan 31, 2026

    • seqBackup

      Public
      Python
      •5•1•1•3•Updated Jan 30, 2026Jan 30, 2026

    • marc_honest

      Public
      Honest broker for mARC db
      Python
      •0•0•0•4•Updated Jan 26, 2026Jan 26, 2026

    • 16S_QIIME2

      Public template
      Snakemake based 16S QIIME2 pipeline
      Python
      •7•1•0•3•Updated Dec 9, 2025Dec 9, 2025

    • cost_estimator

      Public
      An internal utility for keeping track of price estimates
      0•0•0•0•Updated Apr 28, 2025Apr 28, 2025

    • 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

    • TagSequencingPipeline

      Public archive
      Shell
      •5•0•3•2•Updated May 2, 2024May 2, 2024

    • 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

    • 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
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.