Pinned Repositories
DADA2_pipeline_ampliconASVs
DNA amplicon analysis
microbiome_helper
A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
microbiomeExplorer
The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.
OTU-table-to-bubble-plot
R script to create from OTU/ASV tables nice bubble plots for your scientific publications
dada2
Accurate sample inference from amplicon data with single nucleotide resolution
microeco
An R package for data analysis in microbial community ecology
microViz
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
phyloseq
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
Krona
Interactively explore metagenomes and more from a web browser.
AngelicaMiraples's Repositories
AngelicaMiraples/16S_microbiome_analyses
This workflow is used to process sequencing data in the form of demultiplexed fastq files for the full length 16S rRNA gene using pacbio technology
AngelicaMiraples/AngelicaMiraples
AngelicaMiraples/microbiome_helper
A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
AngelicaMiraples/MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
AngelicaMiraples/OTU-table-to-bubble-plot
R script to create from OTU/ASV tables nice bubble plots for your scientific publications