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    27 repositories

    • CHOP_metadata_checker

      Public
      HTML
      •3•0•12•0•Updated Oct 25, 2024Oct 25, 2024

    • PennChopMicrobiomeProgram.github.io

      Public
      Dev board for PCMP
      SCSS
      •0•0•0•0•Updated Oct 23, 2024Oct 23, 2024

    • unassigner

      Public
      Type strain identification for 16S reads
      Python
      •4•4•11•2•Updated Oct 18, 2024Oct 18, 2024

    • SampleRegistry

      Public
      Web application to keep track of samples sequenced
      Python
      •3•0•6•0•Updated Oct 15, 2024Oct 15, 2024

    • PCMP_ITS_pipeline

      Public
      Python
      •1•0•1•1•Updated Sep 25, 2024Sep 25, 2024

    • mirix

      Public
      Quantify the susceptibility of a bacterial community to an antibiotic.
      R
      •1•2•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

    • dnabc

      Public
      Identify DNA barcodes in high-throughput sequencing data files
      Python
      •
      GNU General Public License v2.0
      •6•0•0•0•Updated Jun 25, 2024Jun 25, 2024

    • wfrcwf

      Public
      Python
      •0•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • primertrim

      Public
      Trim primers from reads
      Python
      •0•1•0•1•Updated Jun 5, 2024Jun 5, 2024

    • 16S_QIIME2

      Public template
      Snakemake based 16S QIIME2 pipeline
      Python
      •7•1•0•1•Updated May 17, 2024May 17, 2024

    • TagSequencingPipeline

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

    • adonisplus

      Public
      R
      •
      GNU General Public License v3.0
      •2•2•0•1•Updated Dec 13, 2023Dec 13, 2023

    • ZIBR

      Public
      Zero-Inflated Beta Random Effect model
      R
      •
      Other
      •9•29•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•11•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

    • seqBackup

      Public
      Python
      •4•1•1•0•Updated Jul 22, 2021Jul 22, 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

    • illqc

      Public archive
      Process shotgun metagenomic DNA data for quality
      Python
      •2•1•2•0•Updated Mar 4, 2017Mar 4, 2017

    • PhylogeneticProfiler

      Public archive
      A short wrapper for profiling composition of microbial communities from shotgun metagenomic data.
      Python
      •2•0•2•0•Updated Jan 26, 2017Jan 26, 2017

    • ShotgunPipeline

      Public archive
      Shell
      •2•1•6•0•Updated Sep 16, 2016Sep 16, 2016