Page Index - LangilleLab/microbiome_helper GitHub Wiki
139 page(s) in this GitHub Wiki:
- Home
- 16S Bacteria and Archaea Standard Operating Procedure
- 16S tutorial (chemerin)
- 16S tutorial (long running time)
- 16S tutorial answers
- 16S tutorial for CCBC
- 18S Eukarya Standard Operating Procedure
- 2017 Summer School
- Additional QIIME analysis
- All pages prior to Microbiome Helper 2
- Alpha and beta diversity
- Alternative Processing of Reads with PEAR
- Amplicon Detailed Resources
- Amplicon SOP v2 (qiime2 2018.6)
- Amplicon SOP v2 (qiime2 2018.8)
- Amplicon SOP v2 (qiime2 2019.10)
- Amplicon SOP v2 (qiime2 2019.7)
- Amplicon SOP v2 (qiime2 2020.2)
- Amplicon SOP v2 (qiime2 2020.8)
- Amplicon SOP v2 (qiime2 2022.11)
- Amplicon SOP v2 (qiime2‐2024.5)
- Answers to questions
- BIOC4010 16S Tutorial
- Brief description of scripts
- CBW 2016 Metagenomic Taxonomic Tutorial
- CBW 2016 Metagenomics Functional Tutorial
- CBW 2016 Metagenomics Tutorial Answers
- CBW 2016 PICRUSt tutorial
- CBW 2018 Metagenomic Taxonomic and Functional Composition Tutorial
- CBW 2018 Metagenomic Taxonomic and Functional Composition Tutorial Answers
- CBW 2018 PICRUSt2 Tutorial
- CBW 2018 PICRUSt2 Tutorial Answers
- CBW 2021 Metagenomic Taxonomic and Functional Composition Tutorial
- CBW 2021 Metagenomic Taxonomic and Functional Composition Tutorial Answers
- CBW 2021 PICRUSt2 Tutorial
- CBW 2021 PICRUSt2 Tutorial Answers
- CBW 2024 Advanced Module 1: Introduction to metagenomics and read‐based profiling
- CBW 2024 Advanced Module 2: Metagenomic Assembly and Binning
- CBW 2024 Advanced Module 3: Metagenomic functional annotation
- CBW 2024 Advanced Module 4: Advanced microbiome statistics
- CBW 2024 Beginner Module 1: Introduction to sequencing data analysis
- CBW 2024 Beginner Module 2: Marker gene profiling
- CBW 2024 Beginner Module 3: Microbiome statistics and visualizations
- CBW 2024 Beginner Module 4: Functional prediction and additional analyses
- CBW 2024 workshops
- CBW IMPACTT 2023 answers
- CBW IMPACTT 2023 Microbiome analysis using QIIME2 with 16S data
- CBW IMPACTT Metagenome sequence data analysis with Kraken2 and Phyloseq
- CBW IMPACTT Metagenome sequence data analysis with MMSeqs2 and JarrVis
- CBW IMPACTT workshop tutorials 2023
- CBW workshop 2024 advanced
- CBW workshop 2024 beginner
- CBW‐ICG‐AMB‐Module1
- CBW‐ICG‐AMB‐Module2
- CBW‐ICG‐AMB‐Module3
- CBW‐ICG‐AMB‐Module4
- CBW‐ICG‐BMB‐Module1
- CBW‐ICG‐BMB‐Module2
- CBW‐ICG‐BMB‐Module3
- CBW‐ICG‐BMB‐Module4
- CBW‐IMPACTT metagenomic taxonomic and functional annotation
- CCBC Workshop 2016
- Creating primer specific QIIME 2 taxonomic classifiers
- Creating QIIME 2 Taxonomic Classifiers
- DADA2 16S Chemerin Tutorial
- Download_From_SRA
- Functional profiling
- Home ‐ Microbiome Helper 2
- ICG workshop 2023
- IMPACTT workshop tutorials 2022
- Introduction to Unix
- Introductory Linux Quiz
- IonTorrent Amplicon SOP v1 (qiime2)
- ITS2 Fungi Standard Operating Procedure
- Metagenome sequence data analysis with Kraken2 and Phyloseq
- Metagenomic standard operating procedure
- Metagenomics (answers; IMPACTT 2022)
- Metagenomics (functional annotation; IMPACTT 2022)
- Metagenomics (IMPACTT December 2022)
- Metagenomics (IMPACTT December 2022) Answers
- Metagenomics (IMPACTT December 2022) Assembly
- Metagenomics (IMPACTT December 2022) Pre workshop
- Metagenomics (IMPACTT December 2022) Taxonomic annotation
- Metagenomics (taxonomic annotation; IMPACTT 2022)
- Metagenomics Resources
- Metagenomics Sequencing Pre processing
- Metagenomics standard operating procedure v2
- Metagenomics Standard Operating Procedure v3
- Metagenomics Tutorial (Humann1)
- Metagenomics Tutorial (HUMAnN2)
- Metagenomics Tutorial (Long Running)
- Metagenomics Tutorial (Long Running) Answers
- Metagenomics Tutorial (Older)
- Metagenomics Tutorial (Older) answers
- Metagenomics Tutorial Answers
- Metagenomics Tutorial Answers (HUMAnN1)
- Microbial diversity metrics and data visualization with QIIME2
- Microbiome Amplicon Sequencing Workflow
- Microbiome analysis using QIIME2 with 16S data
- Microbiome for beginners
- Microbiome Helper 2 Amplicon basic statistics and visualisation (qiime2‐amplicon‐2024.10)
- Microbiome Helper 2 Amplicon SOP (qiime2‐amplicon‐2024.10)
- Microbiome Helper 2 Functional annotation of metagenomic reads with HMMs
- Microbiome Helper 2 Metagenomics Standard Operating Procedure Initial Steps
- Microbiome Helper 2 Setting up environments for analysis
- Microbiome Helper Virtual Box
- MicrobiomeHelper Virtual Box
- mSystems paper data
- Old SOPs
- Other Tutorials
- OTU picking
- PacBio CCS Amplicon SOP v1 (qiime2)
- PacBio CCS Amplicon SOP v2 (qiime2 2022.2)
- PacBio CCS Amplicon SOP v2 (qiime2 2024.10)
- Past SOP databases
- PICRUSt tutorial
- PICRUSt Tutorial Answers
- PICRUSt Tutorial with de novo Variants
- PICRUSt workflow
- Predict phenotypes
- QIIME 2 de novo tree creation
- QIIME2 DADA2 Quick Reference
- Quick Introduction to GNU Parallel
- Random Forest Feature Selection Caution
- Random Forest in R with Large Sample Sizes
- Random Forest Tutorial
- Remove chimeric reads
- Remove low quality reads
- Requirements
- Sequence error correction
- Sequence QC
- Setting up an AWS instance with the CBW AMI
- Software References
- STAMP preparation
- STAMPS 2016 PICRUSt Tutorial
- Stitch reads
- Subsampling Metagenomic FASTQs
- Taxonomic composition
- Viromics Pipeline