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Material for course STA426 at UZH, Fall Semester 2019

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Statistical Analysis of High-Throughput Genomic and Transcriptomic Data

Fall/Herbst-semester 2019

Lectures

Mondays 9.00-9.45 (Y27-H-46), 10.00-10.45 (Y27-H-46)

Exercises

Monday 11.00-11.45 (Y01-F-50)

Lecturers

Dr. Hubert Rehrauer, Group Leader of Genome Informatics at FGCZ

Prof. Dr. Mark Robinson, Associate Professor of Statistical Genomics, IMLS, UZH

Katharina Hembach, PhD Student, Robinson Lab, IMLS, UZH

Pierre-Luc Germain, Postdoctoral Fellow, Robinson Lab, IMLS, UZH and Molecular and Behavioral Neuroscience Lab, D-HEST, ETH Zurich

Schedule

Date Lecturer Topic Exercise JC1 JC2
16.09.2019 Mark + Hubert admin; mol. bio. basics R markdown; git(hub)
23.09.2019 Mark interactive technology/statistics session group exercise: technology pull request
30.09.2019 Hubert NGS intro; exploratory data analysis EDA in R
07.10.2019 Hubert mapping Rsubread
14.10.2019 Mark limma + friends linear model simulation + design matrices
21.10.2019 Hubert RNA-seq quantification RSEM
28.10.2019 Kathi hands-on session #1: RNA-seq FASTQC/Salmon/etc. X X
04.11.2019 Mark edgeR+friends 1 basic edgeR/voom
11.11.2019 Mark edgeR+friends 2 GLM/DEXSeq
18.11.2019 Hubert single-cell 1: preprocessing, dim. reduction, clustering scRNA exercise 1
25.11.2019 YYY hands-on session #2: cytometry cytof null comparison X X
02.12.2019 Mark single-cell 2: cell type definition, differential state scRNA exercise 2
09.12.2019 Pierre-Luc hands-on session #3: single-cell RNA-seq full scRNA-seq pipeline X X
16.12.2019 Mark loose ends: HMM, EM, robustness segmentation, peak finding

Useful Links

Simply Statistics blog
Getting Genetics Done blog
Omics Omics blog
Awesome single cell

Course material

Assuming you have git installed locally, you can check out the entire set of course materials with the following command (from command line):

git clone https://github.com/sta426hs2019/material.git

Alternatively, for a ZIP file of the repository, you can click on the (green) 'Clone or download' (top right) and then click 'Download ZIP'.

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Material for course STA426 at UZH, Fall Semester 2019

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