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Concept Course in Bioinformatics
Setup
VPN
Command line interface
Connecting to Cousteau
Disconnecting from Cousteau
R-Studio
Jupyter
Refresher/Preparation Unix
What is Unix?
The command
The file system
Basic file operations
Other useful file operations
Working with files
Searching
Data wrangling
Combining commands
Software
Working on a computing cluster
Clear home directory
Refresher/Preparation R
Calculation and Variables
Types
Mode detection
Vectors
Lists and Data Frames
Names and Indexing
Functions
Program Flow
Loading a Module
Data visualization with
ggplot2
Refresher - Python / Jupyter
Metagenomics Project
Project 1: The gut microbiome composition across age and geography
Project 2: Functionality of microbial communities in different ocean layers
Project solutions
Metagenomics I
Exercise 1: Clustering of sequences into OTUs
Exercise 2: Describing a microbial community at different taxonomic levels
Exercise 3: Calculating alpha-diversity metrics for a microbial community
Metagenomics II
Metagenomics II - Exercise I: Compare differences between samples using beta-diversity indices
Metagenomics II - Exercise II: Principle Components Analysis and Principle Coordinates Analysis
Metagenomics II - Exercise III: Differential abundance testing
Metagenomics II - Exercise IV: Build a random forest model
Metagenomics III
Exercise 1: Explore gene annotations in Marine MAGs
Genomics Project
General tasks
Preliminaries and Setup
Project 1 - DNA-Seq Analysis
Project 2 - RNA-Seq Data Analysis
Genomics I
Transcription and Translation
Sequencing Technologies
Additional Exercises
Genomics II
Bayes Theorem
Additional Exercises
Genomics III
Array-based genomics and transcriptomics
Sequencing-based transcriptomics
Additional Exercises
Single-cell transcriptomics project
Single-cell transcriptomics I
Single-cell transcriptomics II
Protein bioinformatics I
Topics for the exercise
Resources
Protein bioinformatics II
Resources
Protein bioinformatics III
Resources
Network bioinformatics
Exercises
Network bioinformatics II
Exercise
Solution
Exercise
Exercise
#
The exercise is available
here