Blog Archives

Computational genomics course in Berlin: Bisulfite-sequencing and data integration

January 17, 2018
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Bioinformatics platform at Berlin Institute for Medical Systems Biology has been organizing computational genomics courses in Berlin since 2015. This year we will focus on bisulfite sequencing analysis and genomics data integration.The course will cover the following:1) bisulfite-seq analysis (alignment, QC, differential methylation, segmentation)2) integrating and visualizing processed genomics data. These methods can be used for any genomics data set not...

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Poster/cheatsheet for R/BioC package genomation

October 31, 2016
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We prepared a poster/cheatsheet for the bioconductor package genomation, which is a package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments,...

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Annotating sets of genomic intervals with genomic annotations such as chromHMM

August 12, 2016
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Annotating sets of genomic intervals with genomic annotations such as chromHMM

Annotating sets of genomic intervals with genomic annotations such as chromHMM Genomation is an R package to summarize, annotate and visualize genomic intervals. It contains a collection of tools for visualizing and analyzing genome-wide data sets, i.e. RNA-seq, bisulfite sequencing or chromatin-immunoprecipitation followed by sequencing (ChIP-seq) data.Recently we added new...

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methylKit v0.9.6

June 2, 2016
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We released a new version of methylKit, which is a package for DNA methylation analysis with bisulfite-seq data. This version comes with many changes summarized below. you can also have a look at the release notes. The vignette is now converted to HTML and also lives on rpubs.Working with large and/or many filesThis turns out to be more and more...

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methylKit v0.9.6

June 2, 2016
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We released a new version of methylKit, which is a package for DNA methylation analysis with bisulfite-seq data. This version comes with many changes summarized below. you can also have a look at the release notes. The vignette is now converted to...

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Computational Genomics Course in Berlin

May 23, 2016
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Computational Genomics Course in Berlin

Berlin Institute for Medical Systems Biology is organizing a computational genomics course and R programming will be used for most of the practical sessions. The course will cover basic statistics, programming and basic concepts in next-generation sequencing as well as it is applications such as RNA-seq, ChIP-seq, DNA-seq and metagenomics in the context of precision medicine. There will be practical...

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Computational Genomics Course in Berlin

May 23, 2016
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Computational Genomics Course in Berlin

Berlin Institute for Medical Systems Biology is organizing a computational genomics course and R programming will be used for most of the practical sessions. The course will cover basic statistics, programming and basic concepts in next-generation...

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Hands-on computational genomics course in Berlin

July 5, 2015
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Hands-on computational genomics course in Berlin

Berlin Institute for Medical Systems Biology is organizing a computational genomics course and R programming will be used for most practical sessions. The course will cover basic statistics, programming and basic concepts in next-generation sequencing ...

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Segmentation of methylation profiles using methylKit

June 19, 2015
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Segmentation of methylation profiles using methylKit

methylKit is an R package for DNA methylation analysis and annotation using high-throughput bisulfite sequencing data. We recently included a new function in methylKit called methSeg(). The function can segment methylation profiles (methylRaw obje...

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summary, annotation and visualization of genomic intervals with genomation package

February 18, 2014
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We have been working on new R package, genomation, that will help with the analysis of genomic intervals. Briefly, the package contains a collection of tools for visualizing and analyzing genome-wide data sets. The package works with a variet...

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