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Sunagawa Lab Teaching
Upcoming Courses
Sunagawa Lab Block Course Fall 2024: 551-1119-00L Microbial Community Genomics
Previous Courses
Technical Workshop: Software Installation with EasyBuild
What is EasyBuild?
A quick overview of toolchains
EasyConfig files
ConfigureMake example
PythonPackage example
Troubleshooting
Exercise
Computing at the Institute of Microbiology
Computing at the Institute of Microbiology
Computing at the Institute of Microbiology
Technical Workshop: Downstream 16S Analysis
Sunagawa Lab Block Course Fall 2023: 551-1119-00L Microbial Community Genomics
Bioinformatics at the Institute of Microbiology
Setup
Introduction to Unix 1
Introduction to Unix 2
Sequence data
Alignment
Annotation
Phylogenetics
Sunagawa Lab Block Course Fall 2022: 551-1119-00L Microbial Community Genomics
Learn Bioinformatics 2021
Sunagawa Lab Block Course Fall 2021: 551-1119-00L Microbial Community Genomics
Learn Bioinformatics 2020
Software Installation
Introduction to Unix
The Command Line
The File System
Working with Files
Searching for and within Files
Data Wrangling
The Module and Queueing Systems
Introduction to R
R Studio
Calculation and Variables
Lists and Data Frames
Names and Indexing
Functions
Introduction to linear regression
Program Flow
Writing Functions
Packages
Case Study: Analysis of mOTUs Output in R
Data Transformation with
tidyverse
Data visualization with
ggplot2
Statistics
Basic Concepts in Statistics
Fitting Data
Hypothesis Testing
Linear Regression
Sequence Analysis
Sequence Data
Alignment
Quality Control
Short read alignment
Assembly
Annotation
Sunagawa Lab Block Course Fall 2020: 551-1119-00L Microbial Community Genomics
Session 1.10. Describing microbial community structure
Session 1.2. Setup and Linux Introduction
Session 1.5. 16S rRNA analysis using dada2
Introduction to R
Data visualization with
ggplot2
Describing microbial community structure
RepFail study metadata summary
Data Transformation with
tidyverse
Data visualization with
ggplot2
mOTUs OneHealth Workshop August 2019
Infrastructure (20min)
Login to Cluster + mOTUSv2 Installation (60min)
Data (5 min)
Introduction to mOTUs
mOTUs Parameters
Analysis of mOTUs Output in R
mOTUsv2 Database Extension (20 min)
Sunagawa Lab Block Course Fall 2019
Session 1.10. Describing microbial community structure
Session 1.2. Setup and Linux Introduction
Session 1.5. 16S amplicon pipeline
Session 1.6. Introduction to R with RStudio
Index