Fall/Herbst-semester 2022
Mondays 9.00-9.45 (Y27-H-46), 10.00-10.45 (Y27-H-46)
Monday 11.00-11.45 (Y01-F-50)
Dr. Hubert Rehrauer, Group Leader of Genome Informatics at FGCZ
Prof. Dr. Mark Robinson, Associate Professor of Statistical Genomics, DMLS, UZH
| Date | Lecturer | Topic | Exercise | JC1 | JC2 |
|---|---|---|---|---|---|
| 19.09.2022 | Mark + Hubert | admin; mol. bio. basics | quarto; git(hub) | ||
| 26.09.2022 | Mark | interactive technology/statistics session | group exercise: technology pull request | ||
| 03.10.2022 | Hubert | NGS intro; exploratory data analysis | EDA in R | ||
| 10.10.2022 | Mark | limma + friends | linear model simulation + design matrices | ||
| 17.10.2022 | Hubert | mapping | Rsubread | ||
| 24.10.2022 | Hubert | RNA-seq quantification | RSEM | Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis JK DW | X |
| 31.10.2022 | Mark | edgeR+friends 1 | basic edgeR/voom | X | X |
| 07.11.2022 | Mark | edgeR+friends 2 | advanced edgeR/voom | X | X |
| 14.11.2022 | YYY | hands-on session #1: RNA-seq | FASTQC/Salmon/etc. | X | X |
| 21.11.2022 | Hubert | single-cell 1: preprocessing, dim. reduction, clustering | clustering | X | Comparison of Transformations for Single-Cell RNA-Seq Data (GA, RE) |
| 28.11.2022 | YYY | hands-on session #2: cytometry | cytof null comparison | Integrated analysis of multimodal single-cell data (ME, FR) | X |
| 05.12.2022 | Mark | single-cell 2: clustering, marker gene DE | marker gene DE | Differential abundance testing on single-cell data using k-nearest neighbor graphs (DK) | X |
| 12.12.2022 | YYY | hands-on session #3: single-cell RNA-seq (cell type definition, differential state) | full scRNA-seq pipeline | X | Removing unwanted variation from large-scale RNA sequencing data with PRPS (VH, MP) |
| 19.12.2022 | Mark | loose ends: HMM, EM, robustness | segmentation, peak finding | X | X |
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/sta426hs2022/material.git
and get updates by running git pull at any later time in the same directory.
Alternatively, to retrieve a ZIP file of the repository, you can click on the (green) 'Code' button (top right of main panel) and then click 'Download ZIP'.