Blog Archives

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...

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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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Using JavaScript visualization libraries with R

August 26, 2013
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This is a short tutorial on knitr/markdown and JS visualization packages googleVis and rCharts. With these packages you can create web pages with interactive visualizations just using R. This will require minimal or no knowledge of HTML ...

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EpiWorkshop 2013: DNA methylation analysis in R

March 19, 2013
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Elemento Lab at Weill Cornell Medical College organized a workshop on Epigenomics. I had the opportunity to give a tutorial on DNA methylation analysis in R. The tutorial demonstrates how to analyze high-throughput bisulfite sequencing d...

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How to read BSMAP methylation ratio files into R via methylKit

October 5, 2012
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BSMAP is an aligner for bisulfite sequencing reads. It outputs aligned reads as well as methylation ratios per base (via methratio.py script). The methylation ratios can be read into R via methylKit package and regular methylKit analysis can ...

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Updating R but keeping your installed packages

June 28, 2012
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This is probably an issue that has been addressed by many blog posts (including these ones: and ), and can be deduced from R Installation and Administration manual. However, I will post it here for future reference. The problem is that w...

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Plotting differentially methylated bases on an ideogram

June 21, 2012
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(This article was first published on Recipes, scripts and genomics, and kindly contributed to R-bloggers) To leave a comment for the author, please follow the link and comment on their blog: Recipes, scripts and genomics. R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps,...

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