Blog Archives

summary, annotation and visualization of genomic intervals with genomation package

February 18, 2014
By

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 »

Using JavaScript visualization libraries with R

August 26, 2013
By

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 »

EpiWorkshop 2013: DNA methylation analysis in R

March 19, 2013
By

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 »

How to read BSMAP methylation ratio files into R via methylKit

October 5, 2012
By

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 »

Updating R but keeping your installed packages

June 28, 2012
By

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...

Read more »

Plotting differentially methylated bases on an ideogram

June 21, 2012
By

(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 his blog: Recipes, scripts and genomics. R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL,...

Read more »

DNA methylation (RRBS or target capture) analysis with R

February 20, 2012
By

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 »

methylKit: R package for DNA methylation analysis

December 21, 2011
By

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 »

knitr: nice alternative for Sweave

December 17, 2011
By

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 »

Fast(ish) extraction of exon locations from a BED12 file using data.table

March 20, 2011
By

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 »