1 2020 STAT115 Lect1.1 Bioinfo History
2 2020 STAT115 Lect1.2 Big Data Challenge
3 2020 STAT115 Lect1.3 Bioinfo vs Comp Bio
4 2020 STAT115 Lect1.4 Course Info
5 STAT115 Chapter 3.1 Three Generations of Sequencing
6 STAT115 Chapter 3.2 FASTQ and FASTQC
7 STAT115 Chapter 3.4 BLAST and Suffix Arrays
8 STAT115 Chapter 3.5.1 BWT and LF Mapping
9 STAT115 Chapter 3.5.2 Borrows-Wheeler Alignment
10 STAT115 Chapter 3.6 SAM and BAM files
11 2020 STAT115 Lect3.1 RNA-seq Experimental Design
12 2020 STAT115 Lect3.2 RNA-seq Alignment and QC
13 2020 STAT115 Lect3.3 RNA-seq Quantification
14 2020 STAT115 Lect3.4 RNA-seq Read Distribution
15 STAT115 Chapter 5.2 Differential RNA-seq
16 STAT115 Chapter 5.3 Multiple Hypotheses Testing and False Discovery Rate
17 STAT115 Chapter 5.5 Gene Ontology
18 STAT115 Chapter 5.6 Gene Set Enrichment Analyses
19 STAT115 Chapter 6.1/2 Hierarchical Clustering
20 STAT115 Chapter 6.3 K-means Clustering
21 STAT115 Chapter 6.4 Considerations of Kmeans Clustering
22 2020 STAT115 Lect6.1 KNN and MDS
23 2020 STAT115 Lect6.2 PCA
24 STAT115 Chapter 6.5 Batch Effect Removal
25 2020 STAT115 Lect8.1 scRNA-seq
26 2020 STAT115 Lect8.2 Processing and QC scRNA-seq
27 2020 STAT115 Lect8.3 scRNA-seq Clustering and Visualization
28 2020 STAT115 Lect8.4 Differential Expression in scRNA-seq
29 2020 STAT115 Lect9.1 scRNA-seq Batch Effect Removal
30 2020 STAT115 Lect9.2 Gene Expression Module Summary
31 2020 STAT115 Lect9.3 Gene Expression Analysis Scenario
32 STAT115 Chapter 10.1 Transcription Regulation
33 STAT115 Chapter 10.2 Expectation Maximization for Motif Finding
34 STAT115 Chapter 10.3 Gibbs Sampling for Motif Finding
35 STAT115 Chapter 10.4 Motif Finding General Practices
36 STAT115 Chapter 11.1 ChIP-seq
37 STAT115 Chapter 11.2 ChIP-seq Peak Calling with MACS and QC
38 STAT115 Chapter 11.3 TF Interactions from ChIP-seq
39 STAT115 Chapter 11.4 TF Target Genes from ChIP-seq
40 2020 STAT115 Lect12.1 Epigenetics
41 2020 STAT115 Lect12.2 DNA Methylation
42 2020 STAT115 Lect12.3 DNA Methylation Function
43 2020 STAT115 Lect12.4 Nucleosome Positioning
44 2020 STAT115 Lect13.1 Histone Modifications
45 2020 STAT115 Lect13.2 Histone marks on enhancers
46 2020 STAT115 Lect13.3 Histone marks on genes
47 STAT115 Chapter 13.7 DNase-seq
48 2020 STAT115 Lect13.5 ATAC-seq
49 2020 STAT115 Lect15.1 HiC Introduction
50 2020 STAT115 Lect15.2 Topologically Associating Domains
51 2020 STAT115 Lect15.3 Chromatin Compartments
52 2020 STAT115 Lect15.4 Regulatory Network
53 2020 STAT115 Lect16.1 Intro to Single-Cell ATAC-seq
54 2020 STAT115 Lect16.2 Preprocessing and QC scATAC-seq
55 2020 STAT115 Lect16.3 Analysis of scATAC-seq
56 2020 STAT115 Lect16.4 Integrating scATAC-seq with scRNA-seq
57 2020 STAT115 Lect17.1 Module II Review
58 2020 STAT115 Lect17.2 Module II Practice Scenarios
59 Overview of Cistrome Related Tools from Liu Lab
60 2020 STAT115 Lect17.3 SNP and GWAS Intro
61 2020 STAT115 Lect17.4 GWAS Artifacts and eQTL
62 STAT115 Chapter 18.1 Intro Functional Annotate GWAS
63 STAT115 Chapter 18.2 GWAS Functional Enrichment
64 STAT115 Chapter 18.3 Find Causal SNPs
65 STAT115 Chapter 18.4 Predict disease risk
66 STAT115 GWAS Catalogue
67 STAT115 HaploReg
68 STAT115 LD Link
69 STAT115 Chapter 23.1 Introduction to Cancer Genome Analysis
70 STAT115 Chapter 23.2 Cancer. Mutation Characterization
71 STAT115 Chapter 23.3 Cancer Mutation Patterns
72 STAT115 Chapter 23.4 Tumor Purity and Clonality
73 STAT115 Chapter 23.5 Interpret Tumor Mutations
74 STAT115 Chapter 23.6 Find Cancer Genes
75 STAT115 Chapter 23.7 Summary and Future
76 STAT115 OpenCRAVAT Demo
77 STAT115 Chapter 24.1 Tumor Subtypes
78 STAT115 Chapter 24.2 Survival Analysis
79 STAT115 Chapter 24.3 Oncogenes and Tumor Suppressor Mutations
80 STAT115 Chapter 24.4 Cancer Epigenetics
81 2020 STAT115 Lect20.5 Cancer Hallmarks
82 STAT115 Chapter 26.1 Intro to Cancer Immunotherapy
83 STAT115 Chapter 26.2 HLA and Neoantigen Presentation
84 2020 STAT115 Lect22.3 Tumor Immune Deconvolution
85 2020 STAT115 Lect22.4 Immune Receptor Repertoires
86 2020 STAT115 Lect23.1 Immune Signaling
87 2020 STAT115 Lect23.2 Immunotherapy Biomarkers
88 2020 STAT115 Lect23.3 CRISPR Screens
89 2020 STAT115 Lect23.4 CRISPR Screen Computational Challenges
90 2020 STAT115 Lect24.1 Module III Review
91 2020 STAT115 Lect24.2 Course Review
92 2020 STAT115 Lect24.3 Final Logistics