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Adding tutorials to the schedule
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Ahmadrezauf committed Oct 18, 2020
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Expand Up @@ -20,22 +20,22 @@ Monday 11.00-11.45 (remote)

## Schedule

| Date | Lecturer | Topic | Exercise | JC1 | JC2 |
| --- | --- | --- | --- | --- | --- |
| 14.09.2020 | Mark + Hubert | admin; mol. bio. basics | R markdown; git(hub) | <img width=100/> | <img width=100/> |
| 21.09.2020 | Mark | interactive technology/statistics session | group exercise: technology pull request | | |
| 28.09.2020 | Hubert | NGS intro; exploratory data analysis | EDA in R | | |
| 05.10.2020 | Hubert | mapping | Rsubread | | |
| 12.10.2020 | Mark | limma + friends | linear model simulation + design matrices | | |
| 19.10.2020 | Hubert | RNA-seq quantification | RSEM | | |
| 26.10.2020 | Mark | edgeR+friends 1 | basic edgeR/voom | [DUBStepR: correlation-based feature selection for clustering single-cell RNA sequencing data](https://www.biorxiv.org/content/10.1101/2020.10.07.330563v1.full.pdf) (TK, SS, TE) | [From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL](https://www.nature.com/articles/s41540-019-0118-z) (DC, LM) |
| 02.11.2020 | Mark | edgeR+friends 2 | GLM/DEXSeq |[Redefining CpG islands using hidden Markov models](https://academic.oup.com/biostatistics/article/11/3/499/256898) (Zhiwei Dou, Huixin Jin, Peiying Cai)| [Causal Inference in Genetic Trio Studies](https://arxiv.org/abs/2002.09644) (ZS, GW, LN) |
| 09.11.2020 | Kathi | hands-on session #1: RNA-seq | FASTQC/Salmon/etc. | [Statistical significance for genomewide studies](https://www.pnas.org/content/100/16/9440) (RA, HH) | [Identifying signaling genes in spatial single cell expression data](https://www.biorxiv.org/content/10.1101/2020.07.27.221465v2) (YM, KD, GJ) |
| 16.11.2020 | Hubert | single-cell 1: preprocessing, dim. reduction, clustering | | [Testing hypotheses about the microbiome using the linear decomposition model](https://www.biorxiv.org/content/10.1101/229831v3.full.pdf+html) (FS,BO,SA) | [Generalizing RNA velocity to transient cell states through dynamical modeling](https://www.nature.com/articles/s41587-020-0591-3?proof=t) (DP, EH) |
| 23.11.2020 | Helena | hands-on session #2: cytometry | cytof null comparison | [Genome-wide detection of intervals of genetic heterogeneity associated with complex traits](https://academic.oup.com/bioinformatics/article/31/12/i240/216593) (Richard Affolter, Philip Hartout, Martin Emons) | [Empirical Bayes Analysis of a Microarray Experiment](https://www.tandfonline.com/doi/abs/10.1198/016214501753382129) (Jennifer Probst, Eljas Röllin, Lisa Herzog) |
| 30.11.2020 | Mark | single-cell 2: cell type definition, differential state | scRNA exercise 2 | [A Bayesian mixture model for the analysis of allelic expression in single cells](https://doi.org/10.1038/s41467-019-13099-0) (Sneha-Sundar,SmaragdaDimitrakopoulou,marinapanteli) | [scMET: Bayesian modelling of DNA methylation heterogeneity at single-cell resolution](https://www.biorxiv.org/content/10.1101/2020.07.10.196816v2) (MW, RM, DW) |
| 07.12.2020 | Pierre-Luc | hands-on session #3: single-cell RNA-seq | full scRNA-seq pipeline | [ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling](https://academic.oup.com/bioinformatics/article/32/2/260/1743949) (Leonor Schubert, Jonathan Haab, Flavio Rump) | [Detection of differentially abundant cell subpopulations discriminates biological states in scRNA-seq data](https://www.biorxiv.org/content/10.1101/711929v3) (TE, RB, AB)
| 14.12.2020 | Mark | loose ends: HMM, EM, robustness | segmentation, peak finding | [NEBULA: a fast negative binomial mixed model for differential expression and co-expression analyses of large-scale multi-subject single-cell data](https://www.biorxiv.org/content/10.1101/2020.09.24.311662v1) (HML, SCD, SW) | [A test metric for assessing single-cell RNA-seq batch correction](https://www.nature.com/articles/s41592-018-0254-1) (Dimitri Schmid, Lola Kouroma, Jonas Bucher); [AUC-RF: A New Strategy for Genomic Profiling with Random Forest](https://www.karger.com/Article/Abstract/330778) (Jonas Meirer, Dominique Paul) |
| Date | Lecturer | Topic | Exercise | JC1 | JC2 | Tutorial |
| --- | --- | --- | --- | --- | --- | --- |
| 14.09.2020 | Mark + Hubert | admin; mol. bio. basics | R markdown; git(hub) | <img width=100/> | <img width=100/> | <img width=100/> |
| 21.09.2020 | Mark | interactive technology/statistics session | group exercise: technology pull request | | | Exploratory data analysis and visualization with ggplot2 and dplyr |
| 28.09.2020 | Hubert | NGS intro; exploratory data analysis | EDA in R | | | PCA - concept and pitfalls |
| 05.10.2020 | Hubert | mapping | Rsubread | | | Linear regression, diagnostic plots and residual analysis |
| 12.10.2020 | Mark | limma + friends | linear model simulation + design matrices | | | Linear regression, tests and confidence regions, F-value analysis |
| 19.10.2020 | Hubert | RNA-seq quantification | RSEM | | | R-squared and model selection in linear models, Mallow Cp statistic, AIC, BIC criterion |
| 26.10.2020 | Mark | edgeR+friends 1 | basic edgeR/voom | [DUBStepR: correlation-based feature selection for clustering single-cell RNA sequencing data](https://www.biorxiv.org/content/10.1101/2020.10.07.330563v1.full.pdf) (TK, SS, TE) | [From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL](https://www.nature.com/articles/s41540-019-0118-z) (DC, LM) | |
| 02.11.2020 | Mark | edgeR+friends 2 | GLM/DEXSeq |[Redefining CpG islands using hidden Markov models](https://academic.oup.com/biostatistics/article/11/3/499/256898) (Zhiwei Dou, Huixin Jin, Peiying Cai)| [Causal Inference in Genetic Trio Studies](https://arxiv.org/abs/2002.09644) (ZS, GW, LN) | |
| 09.11.2020 | Kathi | hands-on session #1: RNA-seq | FASTQC/Salmon/etc. | [Statistical significance for genomewide studies](https://www.pnas.org/content/100/16/9440) (RA, HH) | [Identifying signaling genes in spatial single cell expression data](https://www.biorxiv.org/content/10.1101/2020.07.27.221465v2) (YM, KD, GJ) | |
| 16.11.2020 | Hubert | single-cell 1: preprocessing, dim. reduction, clustering | | [Testing hypotheses about the microbiome using the linear decomposition model](https://www.biorxiv.org/content/10.1101/229831v3.full.pdf+html) (FS,BO,SA) | [Generalizing RNA velocity to transient cell states through dynamical modeling](https://www.nature.com/articles/s41587-020-0591-3?proof=t) (DP, EH) | |
| 23.11.2020 | Helena | hands-on session #2: cytometry | cytof null comparison | [Genome-wide detection of intervals of genetic heterogeneity associated with complex traits](https://academic.oup.com/bioinformatics/article/31/12/i240/216593) (Richard Affolter, Philip Hartout, Martin Emons) | [Empirical Bayes Analysis of a Microarray Experiment](https://www.tandfonline.com/doi/abs/10.1198/016214501753382129) (Jennifer Probst, Eljas Röllin, Lisa Herzog) | |
| 30.11.2020 | Mark | single-cell 2: cell type definition, differential state | scRNA exercise 2 | [A Bayesian mixture model for the analysis of allelic expression in single cells](https://doi.org/10.1038/s41467-019-13099-0) (Sneha-Sundar,SmaragdaDimitrakopoulou,marinapanteli) | [scMET: Bayesian modelling of DNA methylation heterogeneity at single-cell resolution](https://www.biorxiv.org/content/10.1101/2020.07.10.196816v2) (MW, RM, DW) | |
| 07.12.2020 | Pierre-Luc | hands-on session #3: single-cell RNA-seq | full scRNA-seq pipeline | [ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling](https://academic.oup.com/bioinformatics/article/32/2/260/1743949) (Leonor Schubert, Jonathan Haab, Flavio Rump) | [Detection of differentially abundant cell subpopulations discriminates biological states in scRNA-seq data](https://www.biorxiv.org/content/10.1101/711929v3) (TE, RB, AB) | |
| 14.12.2020 | Mark | loose ends: HMM, EM, robustness | segmentation, peak finding | [NEBULA: a fast negative binomial mixed model for differential expression and co-expression analyses of large-scale multi-subject single-cell data](https://www.biorxiv.org/content/10.1101/2020.09.24.311662v1) (HML, SCD, SW) | [A test metric for assessing single-cell RNA-seq batch correction](https://www.nature.com/articles/s41592-018-0254-1) (Dimitri Schmid, Lola Kouroma, Jonas Bucher); [AUC-RF: A New Strategy for Genomic Profiling with Random Forest](https://www.karger.com/Article/Abstract/330778) (Jonas Meirer, Dominique Paul) | |



Expand All @@ -46,3 +46,4 @@ Assuming you have git installed locally, you can check out the entire set of cou
git clone https://github.com/sta426hs2020/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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