
Week	Tue Lecture	Tue/Thur Labs	Thur Lecture	Sun HW Due
1 (1/27)	Introduction Slides Lecture videos: Bioinfo History Big Data Challenge Bioinfo vs Comp Bio Course Info Other videos: Dynamic programming Reading: Difference between Bioinformatics and Computational Biology Levels of Bioinformatics Research	Odyssey, LINUX, R markdown, BioConductor Please signup for an Odyssey account here! Software carpentry Lab slides: https://github.com/stat115/Lab_2020/tree/master/Lab01 Lab videos: R/bash Introductory Computing Other videos: Unix Shell Python Tutorial	NGS and Read mapping Slides Lecture videos: Sequencing Technologies FASTQ and FASTQC BLAST and Suffix Arrays BWT and LF Mapping BW Alignment SAM and BAM Other videos: Illumina sequencing FASTQ files FASTQC Smith-Waterman algorithm BLAST Suffix trees Suffix arrays BWT FM Index BAM files
2 (2/3)	RNA-seq read mapping, Quantification, Normalization Slides Lecture videos: RNA-seq Experimental Design RNA-seq Alignment and QC RNA-seq Quantification RNA-seq Read Distribution Other videos: RNA-Seq STAR Salmon RPKM, FPKM, TPM	Lab slides: https://github.com/stat115/Lab_2020/tree/master/Lab02 Lab videos: Odyssey/BWA/STAR Lab2 Lab2-DP Other Videos: Statistics in R	Differential expression, FDR, GO Slides Lecture videos: Differential Expression Multiple Hypotheses Testing Gene Ontology Other videos: QQ plot LIMMA DESeq2 Pt1 DESeq2 Pt2 P values False discovery rate Gene Ontology DAVID	HW1 (UNIX, Python, and R)
3 (2/10)	GSEA, Clustering Slides Lecture videos: GSEA Hierarchical Clustering K-means Clustering Consensus Clustering Other videos: Gene Set Enrichment Analyses Heatmaps Hierarchical clustering K-means clustering	RNA-seq QC, PCA, Batch Effects, Gene Set Enrichment Lab videos: Lab 3 video Other videos:	Unsupervised learning, Dimension reduction, Batch effect removal Slides Lecture videos: KNN and MDS PCA Batch Effect Removal Other videos: K nearest neighbors MDS PCA Batch effect removal
4 (2/17)	Classification, Machine learning Slides StatQuest Video Index Machine Learning PlayList Intro to Machine Learning Cross Validation Logistic Regression Regularization Decision Tree Random Forest Support Vector Machines	Pseudoalignment, more Batch Effects, RNA-seq metrics Lab videos: Lab 4 video Other videos:	Single-cell RNA-seq Slides Lecture videos: scRNA-seq Processing and QC Clustering and Annotation Differential Expression Other videos: DropSeq 10X Genomics scRNA-seq Analysis CITE-seq SPLiT-Seq t-SNE Course on scRNA-seq analyses scRNA-seq analyses on BioConductor	HW2 (RNA-Seq)
5 (2/24)	Module I Review Slides Lecture videos: scRNA-seq Batch Effect Removal Gene Expression Module Summary Gene Expression Analysis Scenarios	Seurat, Supervised learning Lab videos: Stat115 Lab5 Lab slides https://github.com/stat115/Lab_2020/tree/master/Lab05 Other videos: Please see the final page of lab slides	[On Module II page]