Publications by altuna
methylKit: R package for DNA methylation analysis
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 functionality allows users to do many of the essential data analysis tasks. The package i...
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DNA methylation (RRBS or target capture) analysis with R
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 and slides on how to do basic RRBS analysis using R and methylKit package. The same m...
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Plotting differentially methylated bases on an ideogram
Related 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 about learning R and many other topics. Click here if you're looking to post or find an R/data-science job. Want to share your content on R-bloggers?...
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Updating R but keeping your installed packages
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 when you update R you usually need to re-install your libraries or change .libPaths()...
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How to read BSMAP methylation ratio files into R via methylKit
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 me...
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EpiWorkshop 2013: DNA methylation analysis in R
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 th...
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Using JavaScript visualization libraries with R
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:knitrgoogleVisrCh...
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summary, annotation and visualization of genomic intervals with genomation package
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 variety of genomic interval file types (BAM, bigWig, BED, GFF and any tabular format containing genomic locati...
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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 objects) or differential methylation profiles (methylDiff objects). Currently the function is available ...
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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 as well as it is applications such as RNA-seq and ChIP-seq. There will be practical sessions eve...
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