Page Index - merckey/microbiome_helper GitHub Wiki

169 page(s) in this GitHub Wiki:

• Home
• 16S Bacteria and Archaea Standard Operating Procedure
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• 16S tutorial (chemerin)
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• 16S tutorial (long running time)
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• 16S tutorial answers
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• 16S tutorial for CCBC
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• 16S tutorials
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• 18S Eukarya Standard Operating Procedure
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• 2017 Summer School
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• Additional QIIME analysis
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• Alpha and beta diversity
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• Alternative Processing of Reads with PEAR
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• Amplicon Detailed Resources
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• Amplicon SOP v2 (qiime2 2018.6)
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• Amplicon SOP v2 (qiime2 2018.8)
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• Amplicon SOP v2 (qiime2 2019.10)
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• Amplicon SOP v2 (qiime2 2019.7)
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• Amplicon SOP v2 (qiime2 2020.2)
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• Amplicon SOP v2 (qiime2 2020.8)
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• Brief description of scripts
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• CBW 2016 Metagenomic Taxonomic Tutorial
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• CBW 2016 Metagenomics Functional Tutorial
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• CBW 2016 Metagenomics Tutorial Answers
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• CBW 2016 PICRUSt tutorial
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• CBW 2018 Metagenomic Taxonomic and Functional Composition Tutorial
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• CBW 2018 Metagenomic Taxonomic and Functional Composition Tutorial Answers
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• CBW 2018 PICRUSt2 Tutorial
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• CBW 2018 PICRUSt2 Tutorial Answers
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• CBW 2021 Metagenomic Taxonomic and Functional Composition Tutorial
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• CBW 2021 PICRUSt2 Tutorial
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• CBW 2021 PICRUSt2 Tutorial Answers
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• CCBC Workshop 2016
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• Creating primer specific QIIME 2 taxonomic classifiers
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• Creating QIIME 2 Taxonomic Classifiers
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• DADA2 16S Chemerin Tutorial
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• Download_From_SRA
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• Functional profiling
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• Introductory Linux Quiz
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• IonTorrent Amplicon SOP v1 (qiime2)
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• ITS2 Fungi Standard Operating Procedure
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• Metagenomic standard operating procedure
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• Metagenomics Resources
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• Metagenomics Sequencing Pre processing
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• Metagenomics standard operating procedure v2
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• Metagenomics Standard Operating Procedure v3
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• Metagenomics Tutorial (Humann1)
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• Metagenomics Tutorial (HUMAnN2)
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• Metagenomics Tutorial (Long Running)
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• Metagenomics Tutorial (Long Running) Answers
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• Metagenomics Tutorial (Older)
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• Metagenomics Tutorial (Older) answers
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• Metagenomics Tutorial Answers
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• Metagenomics Tutorial Answers (HUMAnN1)
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• Microbiome Amplicon Sequencing Workflow
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• Microbiome Helper Virtual Box
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• MicrobiomeHelper Virtual Box
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• mSystems paper data
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• Old SOPs
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• Other Tutorials
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• OTU picking
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• PacBio CCS Amplicon SOP v1 (qiime2)
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• Past SOP databases
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• PICRUSt tutorial
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• PICRUSt Tutorial Answers
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• PICRUSt Tutorial with de novo Variants
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• PICRUSt workflow
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• Predict phenotypes
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• QIIME 2 de novo tree creation
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• QIIME2 DADA2 Quick Reference
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• Quick Introduction to GNU Parallel
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• Random Forest Feature Selection Caution
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• Random Forest in R with Large Sample Sizes
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• Random Forest Tutorial
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• Remove chimeric reads
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• Remove low quality reads
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• Requirements
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• Sequence error correction
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• Sequence QC
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• Software References
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• STAMP preparation
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• STAMPS 2016 PICRUSt Tutorial
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• Stitch reads
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• Subsampling Metagenomic FASTQs
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• Taxonomic composition
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• Viromics Pipeline
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