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...

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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 or JavaScript. You need to have the following R packages and their dependencies installed:knitrgoogleVisrCharts (not on CRAN)The tutorial is organized in four parts. First two...

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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
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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 data ( RRBS is used as an example in the tutorial) with R package methylKit.My slides are below and all of the workshop material...

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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 »

Using ENCODE methylation data (RRBS) in R

March 1, 2013
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Using ENCODE methylation data (RRBS) in R

ENCODE project has generated reduced-representation bilsulfite sequencing data for multiple cell lines. The data is organized in an extended bed format with additional columns denoting % methylation and coverage per base. Luckily, this sort of generic...

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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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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 be performed using the BSMAP data.First,  you need to separate BSMAP methylation ratio file based on methylation context. Cs in CpG,...

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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 when you update R you usually need to re-install your libraries...

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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 »

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