PH525x

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Links to the lectures for the Data Analysis for Genomics course.

See also https://github.com/genomicsclass/labs

Week 1

  1. Overview of what we measure and why: https://www.youtube.com/watch?v=H06H22RMux8
  2. Molecular basis for phenotypic variation: https://www.youtube.com/watch?v=dFtvfzgYfq0
  3. DNA: chromosomes, replication, SNPs, and other variants: https://www.youtube.com/watch?v=OPFWrC_KEGg
  4. Gene expression: https://www.youtube.com/watch?v=X_nKUGRKhlk
  5. Epigenetics: https://www.youtube.com/watch?v=zSOn-cM9xWI
  6. Rstudio: https://www.youtube.com/watch?v=YgqxQFQf1qg
  7. R refresher: https://www.youtube.com/watch?v=yPPAIf7Kgx0
  8. Installing Rstudio and finding help: https://www.youtube.com/watch?v=0uxt6JmLe_Q
  9. Exploratory Data Analysis introduction: https://www.youtube.com/watch?v=-MiCpscqNm0
  10. Histograms: https://www.youtube.com/watch?v=UaXYRf6qtEg
  11. QQ-plot: https://www.youtube.com/watch?v=5F62EwMF26c
  12. Boxplot: https://www.youtube.com/watch?v=Hh-Pd23OmVo
  13. Scatterplot: https://www.youtube.com/watch?v=AaqbNu38gms
  14. Median, MAD, and Spearman correlation: https://www.youtube.com/watch?v=jXyexUUiDgk
  15. Log transformation: https://www.youtube.com/watch?v=G56StIbkMlA
  16. Symmetry of log ratios: https://www.youtube.com/watch?v=euQjNhxMIR8
  17. Plots to avoid: https://www.youtube.com/watch?v=KutseCuGuDI
  18. Avoid pseudo 3D: https://www.youtube.com/watch?v=66Mj2WyPHQg
  19. Examples from genomics: https://www.youtube.com/watch?v=IfO9OdNyEvE
  20. Introduction to probability distribution: https://www.youtube.com/watch?v=govBS0uJ9GA
  21. The normal distribution: https://www.youtube.com/watch?v=IrMIdoZZf5E

Week 2

  1. Microarray technology 1: how hybridisation works: https://www.youtube.com/watch?v=vj3vgkf5rTE
  2. Microarray technology 2: how microarrays work and two colour arrays: https://www.youtube.com/watch?v=pdr6aVFciiM
  3. Microarray technology 2: applications of microarrays in genomics: https://www.youtube.com/watch?v=AXoPsY6kyZM
  4. Next generation sequencing technology 1: brief introduction to the mechanisms of NGS: https://www.youtube.com/watch?v=jQuShWX0ERU
  5. Next generation sequencing technology 2: applications of NGS in genomics: https://www.youtube.com/watch?v=89KFBHER5cM
  6. Basic Bioconductor infrastructure: IRanges: https://www.youtube.com/watch?v=UuS-IRGW-fE
  7. Basic Bioconductor infrastructure: GRanges: https://www.youtube.com/watch?v=CotroQf5hvg
  8. Basic Bioconductor infrastructure: ExpressionSet to SummarizedExperiment: https://www.youtube.com/watch?v=bokZn6qd1kk
  9. Installing from GitHub: https://www.youtube.com/watch?v=8FN1Q2z6nFo
  10. Reading microarray raw data: https://www.youtube.com/watch?v=f7QuRhKD_t8
  11. Microarray EDA: https://www.youtube.com/watch?v=lggp8EzR5nY
  12. Mapping algorithms and software: https://www.youtube.com/watch?v=n7gbw4DjE9o
  13. NGS EDA: https://www.youtube.com/watch?v=2AuDMC6APvM

Week 3

  1. Introduction to statistical inference: https://www.youtube.com/watch?v=Z3W4pNV0wWM
  2. Association tests: https://www.youtube.com/watch?v=h8Rn7rr9M34
  3. T-tests: https://www.youtube.com/watch?v=l18wdf9uTiM
  4. Central Limit Theorem: https://www.youtube.com/watch?v=aYA8ZG-ltqQ
  5. T-tests in practice: https://www.youtube.com/watch?v=7eT_Cq4cm8s
  6. Gene expression example: https://www.youtube.com/watch?v=7GQprJ-F73Y
  7. Inference in practice: https://www.youtube.com/watch?v=bkP7YZqYvmM
  8. Mann-Whitney-Wilcoxon test: https://www.youtube.com/watch?v=mSvuds0xfGc
  9. Monte Carlo simulation: https://www.youtube.com/watch?v=qP9w87RGHAY
  10. Permutations: https://www.youtube.com/watch?v=7kx5kmHi7-8
  11. Introduction to linear models: https://www.youtube.com/watch?v=pw7I70rlkdM
  12. Matrix multiplication: https://www.youtube.com/watch?v=gP7mgpli5t4
  13. Fitting linear models and testing: https://www.youtube.com/watch?v=TSOzvcAgV70
  14. Expressing experimental design using R formula: https://www.youtube.com/watch?v=KpSS2e4Y24w
  15. Basic inference on microarray gene expression I: https://www.youtube.com/watch?v=qmT_Y_7G42U
  16. Basic inference on microarray gene expression II: https://www.youtube.com/watch?v=ayeZPcLXaYU

Week 4

  1. Modelling basics: https://www.youtube.com/watch?v=fxtB8c3u6l8
  2. Application of Poisson: https://www.youtube.com/watch?v=HK7WKsL3c2w
  3. Maximum likelihood estimate: https://www.youtube.com/watch?v=Txc-ybR-fUc
  4. Modelling standard deviations: https://www.youtube.com/watch?v=YMyDG80yIvI
  5. Introduction to microarray background: https://www.youtube.com/watch?v=5r0PWL1aakk
  6. Background model: https://www.youtube.com/watch?v=ToFaVtyGoP4
  7. Different approaches to background: https://www.youtube.com/watch?v=9BCIgRr1KJc
  8. The need for normalisation: https://www.youtube.com/watch?v=DnLZOaERolg
  9. Local regression loess: https://www.youtube.com/watch?v=l81ooxzbz6M
  10. Quantile normalisation: https://www.youtube.com/watch?v=_jd4q17tRAI
  11. Variance stabilising normalisation: https://www.youtube.com/watch?v=ExQkVM4WrYs
  12. When not to normalise: https://www.youtube.com/watch?v=91xrH7cWw8Q
  13. Subset quantile normalisation: https://www.youtube.com/watch?v=YdxszCUhalY
  14. Normalisation for RNA-Seq: https://www.youtube.com/watch?v=HnMJHzDwK4U
  15. Motivating normalisation for microarrays with EDA: https://www.youtube.com/watch?v=HmokevW15QI
  16. Loess normalisation for microarrays: https://www.youtube.com/watch?v=_r0cmw2VjBU
  17. Quantile normalisation for microarrays: https://www.youtube.com/watch?v=UVjgMTG1nIc

Week 5

  1. Distance: https://www.youtube.com/watch?v=MUX98VLM_Y0
  2. Multidimensional scaling: https://www.youtube.com/watch?v=wUkIK17Mc-Y
  3. Clustering: https://www.youtube.com/watch?v=NqH8kUfsFGc
  4. How randomness affects clustering: https://www.youtube.com/watch?v=waqcU-Lxc-I
  5. K-means: https://www.youtube.com/watch?v=pBYANQH9lLc
  6. Gene clustering: https://www.youtube.com/watch?v=yMubXDjw4Bw
  7. Batch effect: https://www.youtube.com/watch?v=qhH_hARH8IM
  8. Distances and clustering I: https://www.youtube.com/watch?v=3e6_OEiLtIo
  9. Distances and clustering II: https://www.youtube.com/watch?v=WFZ4Gxg1rqw
  10. Dimension reduction and heatmaps: https://www.youtube.com/watch?v=ssfuP72qDgo
  11. Conditional expectations: https://www.youtube.com/watch?v=EzGuqhf5XJU
  12. Two variable example: linear regression: https://www.youtube.com/watch?v=hRFYRsWJr3k
  13. K-nearest neighbours: https://www.youtube.com/watch?v=pWJXaVjIMl0
  14. Cross-validation: https://www.youtube.com/watch?v=a0P20iqRp3k

Week 6

  1. Confounding: https://www.youtube.com/watch?v=aqUpNV8pgRs
  2. Confounding in genomics: https://www.youtube.com/watch?v=f8IM3KfUCH0
  3. Modelling batch effects: https://www.youtube.com/watch?v=QE5Qev9AdE8
  4. ComBat: https://www.youtube.com/watch?v=YqoG1wt5ZdU
  5. Factor analysis: https://www.youtube.com/watch?v=_7agXi7xdwE
  6. SVD and PCA: https://www.youtube.com/watch?v=giPJ6caYVSE
  7. PCA example: https://www.youtube.com/watch?v=sHlkVxPWRl4
  8. Microarray example: https://www.youtube.com/watch?v=TjEQUKn3v1g
  9. Surrogate variable analysis: https://www.youtube.com/watch?v=cdJ4Ta4Y5Ow
  10. Introduction to exploring batch effects in R: https://www.youtube.com/watch?v=G6ewaLzGC-c
  11. ComBat in R: https://www.youtube.com/watch?v=YlDrlVHg6JY
  12. SVA in R: https://www.youtube.com/watch?v=Os6t1QQCZZA
  13. PCA and SVD: https://www.youtube.com/watch?v=WYJ-E6rXUWQ

Week 7

  1. Introduction to hierarchical models: https://www.youtube.com/watch?v=SSv1ZKBUhWc
  2. Hierarchical models: baseball example: https://www.youtube.com/watch?v=h9gVIByPyq4
  3. Hierarchical models for genes: https://www.youtube.com/watch?v=Ujq_wqOIAnM
  4. Hierarchical models for genes in practice: https://www.youtube.com/watch?v=ywaI7hdstzU
  5. Using the limma package: https://www.youtube.com/watch?v=5iNUucEn68w
  6. Introduction to multiple testing: https://www.youtube.com/watch?v=5lZqG2lD8b4
  7. Combining null and non-null tests: https://www.youtube.com/watch?v=MQ5F5DpFJGs
  8. Multiple hypothesis testing: https://www.youtube.com/watch?v=RYvguMFsHtw
  9. False discovery rate: https://www.youtube.com/watch?v=cI9TePurn8I
  10. Gene sets: https://www.youtube.com/watch?v=p3JzmaeqiCQ
  11. Summary statistics for gene sets: https://www.youtube.com/watch?v=Ra3JeXSRda0
  12. Hypothesis testing: https://www.youtube.com/watch?v=pZbicSgjLqw
  13. Permutations: https://www.youtube.com/watch?v=_a2fV_kXcBk
  14. Gene set testing in R part I: https://www.youtube.com/watch?v=bfp99aDhjqU
  15. Gene set testing in R part II: https://www.youtube.com/watch?v=IW_YBOe-E0A
  16. Annotating features: https://www.youtube.com/watch?v=WuKtKf4cGBU

Week 8

  1. Visualising NGS data part I: https://www.youtube.com/watch?v=wxeAJ26PeHg
  2. Visualising NGS data part II: https://www.youtube.com/watch?v=DPPXZXagLEw
  3. Visualising NGS data part III: https://www.youtube.com/watch?v=hAyUp5hruug
  4. Making an NGS read count table using Bioconductor: https://www.youtube.com/watch?v=d9RgQ5xbi94
  5. Introduction to DNA methylation: https://www.youtube.com/watch?v=Y0TCJk2QvtA
  6. CpG islands: https://www.youtube.com/watch?v=z-MorcHIhXI
  7. Bisulfite treatment: https://www.youtube.com/watch?v=_FfDsB8vX-c
  8. Measuring methylation from array: https://www.youtube.com/watch?v=V6NqemRSp94
  9. Measuring methylation from sequencing: https://www.youtube.com/watch?v=vFLuM37iKIY
  10. DNA methylation part I: https://www.youtube.com/watch?v=J43x8etwzJo
  11. DNA methylation part II: https://www.youtube.com/watch?v=APISQ5to_BI
  12. Reading 450K files with Minfi: https://www.youtube.com/watch?v=d4P0rVwW5U8
  13. Introduction to ChIP-Seq: https://www.youtube.com/watch?v=uu20X-U7xYk
  14. Computation analysis of ChIP-Seq: https://www.youtube.com/watch?v=tPTwVWW_Kho
  15. Statistical analysis of ChIP-Seq: https://www.youtube.com/watch?v=u-MoGbGJxYs
  16. ChIP-Seq part I: https://www.youtube.com/watch?v=oDWlUGhrjfw
  17. ChIP-Seq part II: https://www.youtube.com/watch?v=pESwMwSBgyo
  18. Introduction to RNA-Seq: https://www.youtube.com/watch?v=269_d0u_gHk
  19. Data generation and simple counts: https://www.youtube.com/watch?v=OUdQZPe3c3U
  20. Model for quantification: https://www.youtube.com/watch?v=vv1UQX9H90w
  21. Transcript quantification: https://www.youtube.com/watch?v=dAl7J_Xazqg
  22. Unstable quantification: https://www.youtube.com/watch?v=eHPcvf2c0B0
  23. RNA-Seq part I: https://www.youtube.com/watch?v=8mf-KOETqhI
  24. RNA-Seq part II: https://www.youtube.com/watch?v=4aAug09cNEk
  25. RNA-Seq part III: https://www.youtube.com/watch?v=H5xjbNIXZpo
  26. SNPs and SNVs: https://www.youtube.com/watch?v=XLBXQS-F9vg
  27. Copy number variants from array: https://www.youtube.com/watch?v=wsmaelR599U
  28. Copy number variants from sequencing: https://www.youtube.com/watch?v=d_9vtBtz1Sw
  29. Variant calling part I: https://www.youtube.com/watch?v=_jJyB4mPZFI
  30. Variant calling part II: https://www.youtube.com/watch?v=clWTO57afsY