Week

Tue Lecture

Tue/Thur Labs

Thur Lecture

Sun HW Due

5 (2/24)

[On Module 1 page]

[On Module 1 page]

Motif finding

Slides

Lecture videos:

Transcription Regulation

Expectation Maximization

Gibbs Sampler

General Practices

Other videos:

Transcription regulation

Post-transcriptional regulation

Gibbs sampling

Expectation Maximization

Motif discovery

 

6

(3/2)

ChIP-seq and integration with expression

Slides

Lecture Videos

ChIP-seq

MACS and QC

TF Interactions

TF Target Genes

Other Videos

ChIP-seq

MACS

Cistrome AP

Cistrome DB

Stat115 Lab 6

 

https://github.com/stat115/Lab_2020/tree/master/Lab06

Epigenetics, DNA methylation

Slides

Lecture Videos: 

Epigenetics

DNA Methylation

DNA Methylation Function

Nucleosome Position

Other Videos

Basic intro1Basic intro2

CpG islands and DNA methylation

DNA methylation and cancer

DNA methylation analyses

 

HW3

(Classification, scRNA-seq)

7

(3/9)

Histone modifications,

Chromatin accessibility

Slides

Lecture videos 

Histone modifications

Histone marks on enhancers

Histone marks on genes

DNase-seq

ATAC-seq

Other videos:

Histone modifications

DNase-seq

ATAC-seq

Macs2, BedTools, Cistrome

Zoom Video

Hidden Markov Model

Slides

Lecture videos

1 2 3 4

Other videos:

HMM Intro

HMM Applications

Forward-backward algorithm

Viterbi algorithm

 

 

 

8 (3/16)

Spring Recess

 

Spring Recess

 

9 (3/23)

Long range chromatin interactions

Slides

Lecture videos

HiC Intro

TADs

Compartments

Regulatory Network

Other videos

HiC (start at 4:30)

Chromosome organization

Loop extrusion model

Enhancer Target Gene Prediction

Lab8 Material

Lab8 Recording

 

scRNA-seq and scATAC-seq integration

Slides

Lecture Videos

Intro to scATAC-seq

Preprocess and QC scATAC-seq

Analysis of scATAC-seq

Integrate scATAC-seq and scRNA-seq

Other videos:

LISA

 

HW4

(ChIP-seq and expression integration)

10 (3/30)

Module II Review 

Slides

Videos:

Module II Review

Practice Questions

GWAS Intro

GWAS Issues and eQTL

 

 

scATAC-seq, SCREEN

 

 

[On Module 3 Page]