Skip to content
Snippets Groups Projects

Changes

Page history
  • New page
  • Templates
    • Update home authored by tamas.schauer's avatar tamas.schauer
    Hide whitespace changes
    Inline Side-by-side
    Showing
    with 13 additions and 9 deletions
    home.md
    View page @ c5897e2e
    ...@@ -28,6 +28,7 @@ BiocManager::install(c("ChIPseeker", "GenomicRanges", "rtracklayer", "TxDb.Hsapi ...@@ -28,6 +28,7 @@ BiocManager::install(c("ChIPseeker", "GenomicRanges", "rtracklayer", "TxDb.Hsapi
    ## Preliminary Schedule ## Preliminary Schedule
    ### Wednesday ### Wednesday
    * 09:00 Introduction * 09:00 Introduction
    * [Reproducible Research](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/presentations/reproducibility_intro/-/blob/main/Reproducibility_Intro.pdf) * [Reproducible Research](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/presentations/reproducibility_intro/-/blob/main/Reproducibility_Intro.pdf)
    * [Introduction to SLURM and HPC](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/hpc-and-slurm) * [Introduction to SLURM and HPC](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/hpc-and-slurm)
    ...@@ -43,28 +44,31 @@ BiocManager::install(c("ChIPseeker", "GenomicRanges", "rtracklayer", "TxDb.Hsapi ...@@ -43,28 +44,31 @@ BiocManager::install(c("ChIPseeker", "GenomicRanges", "rtracklayer", "TxDb.Hsapi
    * Alignment ([Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)) * Alignment ([Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
    * File formats ([fasta](https://en.wikipedia.org/wiki/FASTA_format), [fastq](https://en.wikipedia.org/wiki/FASTQ_format), [bam](https://en.wikipedia.org/wiki/SAM_(file_format))) * File formats ([fasta](https://en.wikipedia.org/wiki/FASTA_format), [fastq](https://en.wikipedia.org/wiki/FASTQ_format), [bam](https://en.wikipedia.org/wiki/SAM_(file_format)))
    ### Thursday * 16:30 [Data processing II](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/data_processing_2)
    * 09:00 [Data processing II](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/data_processing_2)
    * 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))
    * 11:00 [Motif Search](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/motif_search) ### Thursday
    * 9:00 [Motif Search](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/motif_search)
    * consensus peaks with [bedtools](https://bedtools.readthedocs.io/en/latest/) * consensus peaks with [bedtools](https://bedtools.readthedocs.io/en/latest/)
    * find motifs with [Homer](http://homer.ucsd.edu/homer/motif/index.html) * find motifs with [Homer](http://homer.ucsd.edu/homer/motif/index.html)
    * 11:30 Basic [Dataviz with Deeptools](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/dataviz_deeptools) * 10:00 Basic [Dataviz with Deeptools](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/dataviz_deeptools)
    * profile plot * profile plot
    * heatmap * heatmap
    * 12:00 Snakemake final exercise
    * 13:00 Lunch * 11:00 Snakemake final exercise
    * 14:00 External seminar
    * 15:00 Interpretation of workflow results * 12:00 Interpretation of workflow results
    * IGV session * IGV session
    * 16:00 Downstream analysis * 13:00 Lunch
    * 14:00 External seminar
    * 15:00 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)
    ......