16S rRNA amplicon sequencing analysis workflow using QIIME2
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Jun 22, 2021 - Nextflow
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16s
Here are 68 public repositories matching this topic...
Collection of commonly used RDP Tools for easy building
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Dec 30, 2020 - Makefile
Compare different differential abundance and expression methods
metagenomics
rnaseq
auc
proteomics
metabolomics
microbiome
false-positive-control
differential-expression
16s
otu
marker-gene-analysis
relative-abundances
compare-methods
differential-abundance-methods
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Apr 20, 2021 - R
FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
ncbi-taxonomy
taxonomic-classifications
amplicon
16s
ncbi-database
custom-taxonomy
custom-database
metagenomic-classification
centrifuge
taxonomic-classification
kraken2
gtdb
ganon
krakenuniq
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Jun 18, 2021 - Python
The is mostly a wrapper tool using phyloseq and microbiome R packages.
sequencing
metagenomics
microbial-communities
microbiome
amplicon
16s
microbiome-analysis
microbiome-data
core-microbiome
qc-pipeline
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Apr 14, 2021 - R
Various functions for analysis of microbial community data
microbial-communities
microbiome
16s
microbiome-analysis
microbial-ecology
amplicon-sequencing
null-model
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May 3, 2021 - R
Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.
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Jul 18, 2020 - HTML
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Aug 8, 2019 - HTML
Tools for phylogenetic data analysis including visualization and cluster-computing support.
visualization
python
bioinformatics
cross-platform
hpc
slurm
computational-biology
phylogenetics
microbial-genomics
microbiome
16s
qiime
pbs
microbiome-analysis
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Feb 17, 2020 - Python
accessory functions for processing microbial community data
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Jun 27, 2019 - R
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
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Jul 29, 2020 - R
A comprehensive, compact, and automatically curated 16S database
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Nov 28, 2018 - Scala
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Jun 17, 2021 - HTML
Repository for V-Xtractor an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences
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Feb 4, 2021 - Perl
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Feb 5, 2020 - R
Simple script to generate Krona charts for all samples in an OTU table file
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Dec 7, 2018 - Shell
Easy-to-use tool facilitating work with Mothur.
diversity
easy-to-use
microbial-communities
16s
its
fungal
microbial-ecology
microbial
mothur
16s-rrna
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Jul 20, 2020 - JavaScript
code to reproduce AIH results
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May 2, 2018 - R
Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project
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May 12, 2021 - HTML
Working Demo on 16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Visit repo website for HTML output
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Aug 6, 2020 - R
Benbow Lab at Michigan State University, Tutorials/example data for analysis of: 16S data, VCF files
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Aug 12, 2020 - HTML
Reference-based Exact Mapping Amplicon Pipeline
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May 9, 2021 - Jupyter Notebook
workflow
pipeline
slurm
microbiome
16s
microbiome-analysis
dada2
amplicon-sequencing
performance-cluster
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Jun 29, 2018 - R
Some tools made along the way when analyzing 16S amplicon data and metagenomics processing code
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Aug 17, 2018 - Jupyter Notebook
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