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This video by Chloe Herman was made in collaboration with the National Microbiome Data Collaborative (NMDC). The NMDC's mission is to provide a gateway to Findable Accessible Interoperable and Reusable (FAIR) multi-omics microbiome data by leveraging best practices for data curation and processing. For more information and community discussion check out the related QIIME2 Forum post: forum.qiim...

A video introduction to Provenance Replay, software that supports scientific reproducibility, attribution, and collaboration on the QIIME 2 platform. Provenance Replay (AKA `provenance_lib`) parses the computational history (or "provenance") of QIIME 2 Results, letting you: * generate executable scripts for your preferred QIIME 2 interface, allowing users to "replay" prior analyses * report all...

Longitudinal microbiome analysis

Beta diversity visualizations

Alpha diversity visualizations

Getting help with bioinformatics software

Slides: docs.google.com/presentation/d/e/2PACX-1vSpeE9-rcaoOfyD6FuX9CqkzWp7QkQpmxVtIHtXJd8SP5X4uOjKIxclOdXBvbdRUSotP6_F9i2iU8TJ/pub?start=false&loop=false&delayms=3000

Identifying an even sampling depth

Phylogenetic tree construction

This lecture goes more in-depth on unsupervised learning, including a worked-example of polar ordination applied to an example human microbiome data set. The slides for this lecture are available at: docs.google.com/presentation/d/e/2PACX-1vTRMcgTspHpHZuzHvRIZtl9hnHuaA_FmDFskIJPIPQQOCuLpbcGugM4QfsDD8NA_uMQ9l2KEnUpRyXI/pub?start=false&loop=false&delayms=3000 The notes in this video can be found ...

This video introduces unsupervised learning, supervised learning, and core data structures used in machine learning. The slides presented in this video are available at: docs.google.com/presentation/d/e/2PACX-1vRwYPAitVaHz4DDdlIwoTE3IPUup zbEc7PxnH5nT1CsWCKEM2gUrYAv24vOJqqCeo_l7f1OaeLZlQ/pub?start=false&loop=false&delayms=3000

Taxonomic annotation of observed sequences

Filtering feature tables

Computing diversity metrics

Denoising sequence data with DADA2

Microbiome Analysis Methods (part 3)

Microbiome Analysis Methods (part 2)

Microbiome Analysis Methods (part 1)

Importing demultiplexed sequence data

Sequence Homology Searching (part 2)

Sequence Homology Searching (part 3)

Sequence Homology Searching (part 1)

Exploring the tutorial metadata

QIIME 2 Galaxy introduction

Introduction to the Cancer Microbiome Intervention Tutorial data

Text manipulation with regular expressions (part 2)

Text manipulation with regular expressions (part 1)

Introduction to the QIIME 2 Cancer Microbiome Intervention video tutorial

An introduction to QIIME 2