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-SNECourse 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]