Topics

R Basics

Python Basics

Git & Github

Alignment Algorithms

Smith-Waterman algorithm
Multiple sequence alignment algorithms

Data Structures

List
Tree; trie; suffix tree
Suffix array
Graph

Algorithms

Greedy algorithm
Dynamic programming algorithm: Alignment, Sankoff algorithm to small parsimony problem
Combinatorial algorithm: genome rearrangement
Randomized algorithm: motif finding

Statistics

t-test & chi-squared test
Cluster analysis
PCA

Information-theoretic approaches

Entropy, relative entropy and mutual information

NGS applications

Genomic variant
RNA-seq
ChIP-seq
Metagenomics

Biological networks

Gene regulatory network inference
Protein-protein interaction network

Things good to know (not covered in this course)