add prereading

lect03-eda/README.md

@@ -0,0 +1,5 @@
+# Lecture 3 Pre-reading:
+
+* [Chapter 4: Exploratory Data Analysis](https://bookdown.org/rdpeng/artofdatascience/exploratory-data-analysis.html), from The Art of Data Science by Roger Peng and Elizabeth Matsui
+
+* [Section 3 of Chapter 9: Contiguous or supplementary information](https://web.stanford.edu/class/bios221/book/09-chap.html#contiguous-or-supplementary-information), from "Modern Statistics for Modern Biology" by Susan Holmes and Wolfgang Huber:

lect05-twoGroup/README.md

@@ -0,0 +1,8 @@
+# Lecture 5 Pre-reading:
+
+Sections 2-5 of Chapter 6 (Hypothesis Testing) in ["Modern Statistics for Modern Biology"](http://web.stanford.edu/class/bios221/book/) by Susan Holmes and Wolfgang Huber:
+
+* [6.2: Coin-tossing example](https://www.huber.embl.de/msmb/06-chap.html#sec-cointossing)
+* [6.3: Steps of hypothesis testing](https://www.huber.embl.de/msmb/06-chap.html#sec-fivesteps)
+* [6.4: Types of error](https://www.huber.embl.de/msmb/06-chap.html#sec-testing-typesoferror)
+* [6.5: The t-test](https://www.huber.embl.de/msmb/06-chap.html#sec-testing-ttest)

lect08-continuous/README.md

@@ -0,0 +1,11 @@
+# Lecture 8 Pre-reading/listening:
+
+* [Section 18.3: Least Squares Estimates](http://rafalab.dfci.harvard.edu/dsbook/linear-models.html#lse) in "Introduction to Data Science" by Rafael Irizarry
+* [Collinearity & Confounding](http://genomicsclass.github.io/book/pages/collinearity.html) section from Chapter 5 of "Biomedical Data Science" by Rafael Irizarry
+* [This 2.5 minute audio clip introducing limma](https://www.youtube.com/embed/ZRet1oeGiUU?&end=150) from [Kasper Hansen's course "Bioconductor for Genomic Data Science"](https://kasperdanielhansen.github.io/genbioconductor/):
+
+<p align="center">
+<a href="https://www.youtube.com/embed/ZRet1oeGiUU?&end=150"><img src="img/limmavideoscreenshot.png" alt="limma video screenshot"></a>
+</p>
+
+

lect09-multipleTesting/README.md

@@ -0,0 +1,14 @@
+# Lecture 9 Pre-reading/watching:
+
+* [This 14 minute screencast demonstrating design matrix construction and limma in action](https://www.youtube.com/embed/ZRet1oeGiUU?&start=150) (a continuation from last lecture's material) from Kasper Hansen's course ["Bioconductor for Genomic Data Science"](https://kasperdanielhansen.github.io/genbioconductor/):
+
+<p align="center">
+<a href="https://www.youtube.com/embed/ZRet1oeGiUU?&start=150"><img src="img/limmavideoscreenshot.png" alt="limma video screenshot"></a>
+</p>
+
+* Sections 7-9 in Chapter 6 (Hypothesis Testing) in ["Modern Statistics for Modern Biology"](http://web.stanford.edu/class/bios221/book/) by Susan Holmes and Wolfgang Huber:
+
+  * [6.7: Multiple testing](https://www.huber.embl.de/msmb/06-chap.html#multiple-testing)
+  * [6.8: The family wise error rate](https://www.huber.embl.de/msmb/06-chap.html#sec-testing-FWER)
+  * [6.9: The false discovery rate](https://www.huber.embl.de/msmb/06-chap.html#the-false-discovery-rate)
+

lect10-RNAseq/README.md

@@ -0,0 +1,16 @@
+# Lecture 10 Pre-reading:
+
+* Sections 1-3 in Chapter 1 (Generative Models for Discrete Data) in ["Modern Statistics for Modern Biology"](http://web.stanford.edu/class/bios221/book/) by Susan Holmes and Wolfgang Huber:
+
+  * [1.1: Overview & goals](https://www.huber.embl.de/msmb/01-chap.html)
+  * [1.2: A real example](https://www.huber.embl.de/msmb/01-chap.html#a-real-example)
+  * [1.3: Using discrete probability models](https://www.huber.embl.de/msmb/01-chap.html#using-discrete-probability-models)
+
+* Chapter 8 (High-Throughput Count data) in in ["Modern Statistics for Modern Biology"](http://web.stanford.edu/class/bios221/book/) by Susan Holmes and Wolfgang Huber:
+
+  * [8.1: High-Throughput Count Data](https://www.huber.embl.de/msmb/01-chap.html)
+
+  * [8.4: Modeling count data](https://www.huber.embl.de/msmb/08-chap.html#modeling-count-data)
+
+* [This deep dive comparative analysis of RNA-seq data with several different approaches](https://github.com/STAT540-UBC/resources/blob/main/rnaseqdiffex-examples/examples-RNAseq.md)
+

lect11-epigenetics/README.md

@@ -0,0 +1,9 @@
+# Lecture 11 Pre-reading/watching:
+
+* [This 8.5 minute video: "A Gentle Introduction to ChIP-seq"](https://www.youtube.com/embed/nkWGmaYRues) from the StatQuest YouTube channel:
+
+<p align="center">
+<a href="https://www.youtube.com/embed/nkWGmaYRues"><img src="img/chipseqvideoscreenshot.png" alt="chipseq video screenshot"></a>
+</p>
+
+* [Chapter 33: DNA Methylation, from "Handbook of Statistical Genomics", by Hansen, Siegmund and Lin](https://go.exlibris.link/R1hjRtdV) - link to full text of the book, which is available online via UBC Library after CWL login

lect12-gsea/README.md

@@ -0,0 +1,5 @@
+# Lecture 12 Pre-reading:
+
+Section 3 in Chapter 10 (Generative Models for Discrete Data) in ["Modern Statistics for Modern Biology"](http://web.stanford.edu/class/bios221/book/) by Susan Holmes and Wolfgang Huber:
+
+[10.3: From gene set enrichment to networks](https://web.stanford.edu/class/bios221/book/10-chap.html#from-gene-set-enrichment-to-networks)