Fall/Herbst-semester 2021
Mondays 9.00-9.45 (Y27-H-46), 10.00-10.45 (Y27-H-46)
Monday 11.00-11.45 (Y27-H-46)
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 |
|---|---|---|---|---|---|
| 20.09.2021 | Mark + Hubert | admin; mol. bio. basics | R markdown; git(hub) | ||
| 27.09.2021 | Mark | interactive technology/statistics session | group exercise: technology pull request | ||
| 04.10.2021 | Hubert | NGS intro; exploratory data analysis | EDA in R | ||
| 11.10.2021 | Hubert | mapping | Rsubread | ||
| 18.10.2021 | Mark | limma + friends | linear model simulation + design matrices | ||
| 25.10.2021 | Hubert | RNA-seq quantification | RSEM | X | X |
| 01.11.2021 | Mark | edgeR+friends 1 | basic edgeR/voom | OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data (BT, KN) | Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ) (RM, DS) |
| 08.11.2021 | Mark | edgeR+friends 2 | advanced edgeR/voom | ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system (TB, OF) | X |
| 15.11.2021 | Mark | hands-on session #1: RNA-seq | FASTQC/Salmon/etc. | Differential abundance testing on single-cell data using k-nearest neighbor graphs (VW, JL) | X |
| 22.11.2021 | Hubert | single-cell 1: preprocessing, dim. reduction, clustering | clustering | A variable selection approach for highly correlated predictors in high-dimensional genomic data (SV,PN) | X |
| 29.11.2021 | Mark | hands-on session #2: cytometry | cytof null comparison | A test metric for assessing single-cell RNA-seq batch correction (YX,ZL) | Identifying cellular-to-phenotype associations by elucidating hierarchical relationships in high-dimensional cytometry data (TJ, AP) |
| 06.12.2021 | Mark | single-cell 2: clustering, marker gene DE | marker gene DE | Causal inference in genetic trio studies (CG, DC) | Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling (JW) |
| 13.12.2021 | Pierre-Luc | hands-on session #3: single-cell RNA-seq (cell type definition, differential state) | full scRNA-seq pipeline | CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes (KC, SG) | X |
| 20.12.2021 | 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/sta426hs2020/material.git
and get updates by running git pull at any later time in the same directory.
Alternatively, for a ZIP file of the repository, you can click on the (green) 'Code' button (top right of main panel) and then click 'Download ZIP'.