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* 13:00 Lunch
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* 14:00 External seminar
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* 15:00 Downstream analysis
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* Introduction to [R](https://www.r-project.org), [Rmarkdown](https://rmarkdown.rstudio.com) and [Bioconductor](https://bioconductor.org)
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* 15:00 Working with peaks in R
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We gonna use the course data for downstream analysis.
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* [Introduction](https://github.com/FranziG/Working-with-Peaks-in-R/blob/master/presentations/Introduction%20to%20R%20and%20Bioconductor.pdf) to [R](https://www.r-project.org), [Rmarkdown](https://rmarkdown.rstudio.com) and [Bioconductor](https://bioconductor.org)
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* [Import](https://htmlpreview.github.io/?https://github.com/FranziG/Working-with-Peaks-in-R/blob/master/ImportPeaks.html) MACS peak files into R and filtering
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* [GenomicRanges](https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html)
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* [ENCODE blacklisted regions](https://doi.org/10.1038/s41598-019-45839-z) and how to remove them
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* Handling multiple BED files with [GRangesLists](https://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/GenomicRanges/html/GRangesList-class.html)
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* Consensus peak sets, reproducible peaks and peak unions
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* Visualizing peak subsets/overlaps ([UpSetR](https://github.com/hms-dbmi/UpSetR), [VennDiagram](https://cran.r-project.org/web/packages/VennDiagram/VennDiagram.pdf), [eulerr]( https://cran.r-project.org/web/packages/eulerr/vignettes/introduction.html))
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### Friday
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* 09:00 Data visualization
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* R graphics
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* Peak annotation and comparison ([ChIPseeker](http://bioconductor.org/packages/devel/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html))
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* 09:00 Working with peaks in R continued
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* A short introduction into [ggplot2](https://ggplot2-book.org/)
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* Peak annotation and comparison ([ChIPpeakanno](https://www.bioconductor.org/packages/devel/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.html), [ChIPseeker](http://bioconductor.org/packages/devel/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html))
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* Inferring biological meaning with over-representation analysis ([ClusterProfiler](https://yulab-smu.top/biomedical-knowledge-mining-book/enrichment-overview.html))
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* 13:00 Lunch
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* 14:00 External seminar
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* 15:00 Q&A |
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* 15:00 Q&Aeeeeeeee |
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