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2020 STAT115 Lect1.1 Bioinfo History
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STAT115 2020
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- 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
