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
Emanuel Sonder, PhD Student, D-HEST, ETHZ
Helena Crowell, PhD Student, DMLS, UZH
Anthony Sonrel, PhD Student, 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 | X | X |
| 31.10.2022 | Mark | edgeR+friends 1 | basic edgeR/voom | Cell2location maps fine-grained cell types in spatial transcriptomics (JS, GM) | SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes (PWG, FP) |
| 07.11.2022 | Emanuel | hands-on session #1: RNA-seq | FASTQC/Salmon/etc. | Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics (GB, ML) | Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis JK DW |
| 14.11.2022 | Mark | edgeR+friends 2 | advanced edgeR/voom | Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq (LM, YM) | EAGLE: Explicit Alternative Genome Likelihood Evaluator - BMC Medical Genomics (EJ, SL) |
| 21.11.2022 | Hubert | single-cell 1: preprocessing, dim. reduction, clustering | clustering | SpatialDM: Rapid identification of spatially co-expressed ligand-receptor reveals cell-cell communication patterns (JO, YW) | Comparison of Transformations for Single-Cell RNA-Seq Data (GA, RE) |
| 28.11.2022 | Mark/Helena | 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) | Redefining CpG islands using Hidden Markov Models (LL, JF) |
| 12.12.2022 | Anthony | hands-on session #3: single-cell RNA-seq (cell type definition, differential state) | full scRNA-seq pipeline | Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 (AA) | Removing unwanted variation from large-scale RNA sequencing data with PRPS (VH, MP) |
| 19.12.2022 | Mark | spatial omics | spatial statistics | 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'.