... | @@ -48,17 +48,20 @@ BiocManager::install(c("ChIPseeker", "GenomicRanges", "rtracklayer", "TxDb.Hsapi |
... | @@ -48,17 +48,20 @@ BiocManager::install(c("ChIPseeker", "GenomicRanges", "rtracklayer", "TxDb.Hsapi |
|
* Genome coverage ([Deeptools](https://deeptools.readthedocs.io/en/develop/))
|
|
* Genome coverage ([Deeptools](https://deeptools.readthedocs.io/en/develop/))
|
|
* Peak finding ([MACS2](https://github.com/macs3-project/MACS))
|
|
* Peak finding ([MACS2](https://github.com/macs3-project/MACS))
|
|
* File formats ([bed](https://en.wikipedia.org/wiki/BED_(file_format)), [bedgraph](https://genome.ucsc.edu/goldenpath/help/bedgraph.html))
|
|
* File formats ([bed](https://en.wikipedia.org/wiki/BED_(file_format)), [bedgraph](https://genome.ucsc.edu/goldenpath/help/bedgraph.html))
|
|
|
|
* 10:00 [Motif Search](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/motif_search)
|
|
* 11:00 Basic [Dataviz with Deeptools](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/dataviz_deeptools)
|
|
* 11:00 Basic [Dataviz with Deeptools](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/dataviz_deeptools)
|
|
* 12:00 Snakemake final exercise
|
|
* 12:00 Snakemake final exercise
|
|
* 13:00 Lunch
|
|
* 13:00 Lunch
|
|
* 14:00 External seminar
|
|
* 14:00 External seminar
|
|
* 15:00 Downstream analysis
|
|
* 15:00 Interpretation of workflow results
|
|
|
|
* IGV session
|
|
|
|
* 16:00 Downstream analysis
|
|
* Introduction to [R](https://www.r-project.org), [Rmarkdown](https://rmarkdown.rstudio.com) and [Bioconductor](https://bioconductor.org)
|
|
* Introduction to [R](https://www.r-project.org), [Rmarkdown](https://rmarkdown.rstudio.com) and [Bioconductor](https://bioconductor.org)
|
|
* [GenomicRanges](https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html)
|
|
* [GenomicRanges](https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html)
|
|
|
|
|
|
### Friday
|
|
### Friday
|
|
* 09:00 Data visualization
|
|
* 09:00 Data visualization
|
|
* R graphics ([ggplot2](https://ggplot2.tidyverse.org))
|
|
* R graphics
|
|
* Peak annotation and comparison ([ChIPseeker](http://bioconductor.org/packages/devel/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html))
|
|
* Peak annotation and comparison ([ChIPseeker](http://bioconductor.org/packages/devel/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html))
|
|
* 13:00 Lunch
|
|
* 13:00 Lunch
|
|
* 14:00 External seminar
|
|
* 14:00 External seminar
|
... | | ... | |