The purpose of this repository is to store R scripts that were used for 16S community compositional analyses.
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Apr 1, 2024 - R
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dada2
Here are 42 public repositories matching this topic...
A repository containing a demo microbiome workflow for R and Python
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Apr 11, 2018 - Jupyter Notebook
This repositorey contain the dada2 pipeline used to process the illumina sequence reads in the manuscript "Temporal variability in the growth-enhancing effects of different bacteria within the microbiome of the diatom Actinocyclus sp." (DOI: 10.3389/fmicb.2023.1230349)
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Jul 21, 2023
CUSO Microbiome analysis workshop 2020
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Jul 13, 2021 - R
Microbiome analysis pipeline with reference tutorial. This code was written in October 2024 to process rRNA marker gene data (16S and ITS) from rhizosphere soil samples.
unite high-throughput-sequencing 16s soil-sample rrna taxonomy-assignment its microbiome-analysis mafft dada2 marker-gene-analysis greengenes qiime2 microbiome-workflow fasttree microbiome-analysis-pipelines soil-microbiome rhizospheres
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Feb 4, 2025 - Shell
This is repository of amplicon sequencing data and bioinformatics pipeline codes for the nectar microbiome of Monkey Flowers.
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Jun 22, 2023
Here we discuss strategies and workflows to analyse metagenomics datasets
python r pipelines metagenomics kraken dada2 amplicon-sequencing qiime2 deblur bracken epi2me shotgun-metagenomics
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Dec 25, 2023
neonMicrobe: Processing NEON soil microbe marker gene sequence data into ASV tables, duplicated from https://github.com/claraqin/neonMicrobe
bioinformatics neon r-package marker-genes macroecology biogeography dada2 soil-microbiome neonmicrobe
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Jan 15, 2023 - HTML
Metabarcoding analysis pipeline, using DADA2 and qiime2
bioinformatics bioinformatics-pipeline metabarcoding dada2 cutadapt qiime2 taxonomic-profiling metabarcoding-data
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Jan 9, 2024 - Shell
Introduction to 16S Amplicon Sequencing Data Analysis using DADA2
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Jul 28, 2023
Analysis of 16S rRNA (dada2 amplicon sequence variants) from human volunteers given various vaccines following two different antibiotics treatments compared to no antibiotics.
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Jun 30, 2021 - HTML
Reconstructing a dada2 pipeline with batch processing using an OOP design
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Apr 12, 2021 - R
Modified dada2 script, used for master's thesis project. Takes fast2 files and outputs ASV table, taxonomy table, phylogenetic tree, and input files for PICRUSt2
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Nov 13, 2021
Metabarcoding and 16S rRNA Gene Sequencing (BIOF-Mic101)
statistical-analysis microbiome metabarcoding 16s microbiome-analysis dada2 microbiome-data metaanalysis
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Feb 24, 2025
Code and repository links for Klein & Frühe et al. 2024
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Feb 16, 2025 - R
Docker convenience image containing R and the DADA2 package (plus dependencies), used for processing amplicon data.
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Feb 12, 2025 - Dockerfile
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Oct 11, 2024 - R
Workflow stages and data for Morando, Magasin et al. 2024
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Feb 4, 2025 - R
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