qiime

There are 2 repositories under qiime topic.

• biocore / empress

  A fast and scalable phylogenetic tree viewer for microbiome data analysis

  phylogenyvisualizationmicrobiometree-plotbioinformaticsordinationbiplotqiime2qiime
  Language:JavaScript 45

• biocore / redbiom

  Sample search by metadata and features

  biombioinformaticsmicrobiomeqiime
  Language:Python 43

• biocore / qurro

  Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

  microbiomevisualizationqiimebioinformatics
  Language:JavaScript 30

• Joseph7e / Assign-Taxonomy-with-BLAST

  Assign taxonomy with blast, can be used for qiime

  taxonomy-assignmentqiimeblastncbi-taxonomyncbi-blastncbi-database
  Language:Python 19

• smdabdoub / phylotoast

  Tools for phylogenetic data analysis including visualization and cluster-computing support.

  pythonphylogeneticsqiimevisualization16smicrobiomemicrobiome-analysismicrobial-genomicsbioinformaticscomputational-biologycross-platformhpcpbsslurm
  Language:Python 12

• ElDeveloper / dogs

  Companion notebooks for "Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks"

  microbiomenotebookjupyerqiimeibd16s
  Language:Jupyter Notebook 11

• Xcelris-Labs-Ltd / Publication-ready-taxonomic-charts-from-QIIME

  Ultra fast program to generate publication ready taxonomic pie charts from QIIME.

  pie-chartqiimetaxonomypython
  Language:Python 5

• attayeb / auto-q

  Auto-q Qiime Analysis Automating Script

  qiimefastq-filesanalysis
  Language:Python 3

• hohonuuli / qiime1

  Docker container for running qiime

  qiimedocker
  3

• ResearchIT / qiime2

  Singularity Recipe for QIIME 2

  qiimesingularity
  Language:Roff 3

• tianrenmao / 16S-18S-ITS-ASAP

  This is an automatic pipeline for analysis of amplicon sequence data including 16S, 18S and ITS. It wraps QIIME commands and complements them with additional analysis where QIIME is not good at, such as combine multiple sequencing runs, OTU clustering and chimeric removal with UP ARSE, alignment filtering with Gblock, removing Chloroplast sequences.

  16s-rrna18s-rrnaits-sequenceamplicon-sequencingqiimewrapperautomatic-pipeline
  Language:Perl 3

• digsci / biolab

  Bioinformatics pipeline for analysis of diatom sequenced data

  bioinformaticsjupyter-notebookqiime
  Language:Jupyter Notebook 2

• ElDeveloper / phd-thesis

  Doctoral dissertation

  microbiomeemperorqiime
  Language:TeX 2

• nishattasnim11 / 16S_soilgut

  MSc - 16S sequence datasets, amplicon analysis, and stats

  qiimeotu-tablephyloseqggplot2
  Language:R 2

• astrdhr / metagenomics-soil

  BSc project: metagenomic analysis of urban park soil. Breakdown of some of the code I used can be viewed on this website:

  16s-rrnametagenomicsmetagenomic-analysisqiime
  Language:Shell 1

• biocore / q2-ili

  QIIME2 plugin for `ili

  microbiomeqiimevisualization
  Language:Python 1

• joowkim / 16s-data-analysis-using-Qiime1

  qiimedeprecated
  Language:Jupyter Notebook 1

• sghignone / R.Qiime_MaarjAM

  A semi-automated protocol to get Qiime-formatted MaarjAM database of Arbuscular Mycorrhizal Fungi

  qiimemaarjam
  Language:R 1

• andrew10043 / qiimeTutorials

  Tutorials on microbiome analysis using the Quantitative Insights Into Microbial Ecology (QIIME) platform

  pythonqiimemicrobiome
  Language:Shell 0

• jessyboricua / ancient-caribbean-microbiomes

  Analysis of DNA sequencing data obtained from ancient feces of Huecoids and Saladoids, two cultures that lived in the Caribbean before the arrival of Europeans to the region.

  bioinformaticsbiologydatadata-analysismicrobiomepythonqiime
  0

• akshayparopkari / phylotoast

  Tools for phylogenetic data analysis including visualization and cluster-computing support.

  python16svisualizationphylogeneticsqiimemicrobial-genomicsmicrobiome-analysismicrobiomebioinformatics
  Language:Python

• Franky1 / microbiome

  Streamlit app forked for debugging purposes

  qiimestreamlitstreamlit-sharing
  Language:Python

• glickmac / Microbiome_Demo

  A repository containing a demo microbiome workflow for R and Python

  16s-rrnadada2jupyter-notebookmicrobiomemicrobiome-workflowqiimetutorial
  Language:Jupyter Notebook

• glickmac / OTU_Groupings

  qiimemergingotusgreengenesmicrobiomebiomsilvaworkflow
  Language:Shell

• olabiyi / qiime1-scripts

  Bash scripts for running QIIME 1.9 and a Snakemake workflow to automate it using singularity container images.

  microbiome-analysisqiimesingularity-containers
  Language:Shell

• segrelab / MiCoNE-pipeline-paper

  The source code for the MIND pipeline paper

  16s-rrnadata-analysismicrobiomeqiimeqiime2
  Language:HTML