Blog Archives

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....

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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...

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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...

Read more »

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...

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Computational Genomics Course in Berlin

May 23, 2016
By
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 ...

Read more »

Hands-on computational genomics course in Berlin

July 5, 2015
By
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 ...

Read more »

Segmentation of methylation profiles using methylKit

June 19, 2015
By
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 objects) or differential methylation profiles (methylDiff objects). Currently the function is available on a different branch for development. You can install the version of methylKit that...

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Segmentation of methylation profiles using methylKit

June 19, 2015
By
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...

Read more »

summary, annotation and visualization of genomic intervals with genomation package

February 18, 2014
By

We have been working on a 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 variety of genomic interval file types (BAM, bigWig, BED, GFF and any tabular format containing genomic locations) and enables easy summarization...

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