The purpose of this repository is to store R scripts that were used for 16S community compositional analyses.
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Updated
Apr 1, 2024 - R
The purpose of this repository is to store R scripts that were used for 16S community compositional analyses.
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)
A repository containing a demo microbiome workflow for R and Python
CUSO Microbiome analysis workshop 2020
This is repository of amplicon sequencing data and bioinformatics pipeline codes for the nectar microbiome of Monkey Flowers.
Here we discuss strategies and workflows to analyse metagenomics datasets
Metabarcoding analysis pipeline, using DADA2 and qiime2
neonMicrobe: Processing NEON soil microbe marker gene sequence data into ASV tables, duplicated from https://github.com/claraqin/neonMicrobe
En este repositorio se encuentran todos los scripts utilizados para mi tesis de licenciatura, titulada: "Análisis de perfiles funcionales de la microbiota intestinal de pacientes con trastorno depresivo mayor", la cual utiliza un lenguaje de programación en R y Phyton.
Analysis of 16S rRNA (dada2 amplicon sequence variants) from human volunteers given various vaccines following two different antibiotics treatments compared to no antibiotics.
Reconstructing a dada2 pipeline with batch processing using an OOP design
Introduction to 16S Amplicon Sequencing Data Analysis using DADA2
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
DADA2 pipeline for nitrogenase (nifH) amplicon sequences (Illumina paired-end)
Docker convenience image containing R and the DADA2 package (plus dependencies), used for processing amplicon data.
Workflow stages and data for Morando, Magasin et al. 2024
Code and repository links for Klein & Frühe et al. 2024
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