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* 13:00 Lunch
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* 14:00 External seminar
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* 15:00 Working with peaks in R\
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* 15:00 [Working with peaks in R](https://github.com/FranziG/Working-with-Peaks-in-R/blob/master/presentations/Working%20with%20peaks%20in%20R_presentation.pdf)\
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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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* [Handling multiple BED file](https://htmlpreview.github.io/?https://github.com/FranziG/Working-with-Peaks-in-R/blob/master/PeakOverlapsAndAnnotation.html) 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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