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. ... [Read more...]

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 ... [Read more...]

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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 ... [Read more...]

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...]

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... [Read more...]

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 ... [Read more...]

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...]

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...]

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... [Read more...]

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 ... [Read more...]

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... [Read more...]

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 ... [Read more...]

This is probably an issue that has been addressed by many blog posts (including these ones: [link1] and [link2]), and can be deduced from R Installation and Administration manual. However, I will post it here for future reference. The problem is that w... [Read more...]

[This article was first published on Recipes, scripts and genomics, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to [Read more...]

Reduced Representation Bisulfite sequencing (RRBS) is a popular technique for measuring methylation levels across genome. Although it does not have the full genome coverage, it covers many important regions for methylation. Below, I shared a tutorial a... [Read more...]

High-throughput bisulfite sequencing based methods are popular for measuring genome-wide DNA methylation levels. Here is an R package that helps with the analysis of such DNA methylation data. Although, it is still under heavy development current funct... [Read more...]

I recently discovered knitr for dynamic report generation in R. It seems like a very powerful alternative to Sweave. Particularly, I am interested in png graphic device support (it supports more than 20 graphic devices) and R code formatting.Check it o... [Read more...]

Here is a fast R function to extract exon locations from a BED12 file. Note that fast is a relative term, the function below is fast enough for me, may not be fast enough for others :) Anyway, a BED12 file typically has locations of genomic features (t... [Read more...]

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