Articles by altuna

Computational genomics course in Berlin: Bisulfite-sequencing and data integration

January 17, 2018 | altuna

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...]

Poster/cheatsheet for R/BioC package genomation

October 31, 2016 | altuna

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...]

Annotating sets of genomic intervals with genomic annotations such as chromHMM

August 12, 2016 | altuna

Annotating sets of genomic intervals with genomic annotations such as chromHMM Genomation is an R package to summarize, annotate and visualize genomic intervals. It contains a collection of tools for visualizing and analyzing genome-wide data sets, i.e. RNA-seq, bisulfite sequencing or chromatin-immunoprecipitation followed by sequencing (ChIP-seq) data.Recently we ...
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methylKit v0.9.6

June 2, 2016 | altuna

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...]

methylKit v0.9.6

June 2, 2016 | altuna

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...]

Computational Genomics Course in Berlin

May 23, 2016 | altuna

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...]

Computational Genomics Course in Berlin

May 23, 2016 | altuna

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...]

Hands-on computational genomics course in Berlin

July 5, 2015 | altuna

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...]

Updating R but keeping your installed packages

June 28, 2012 | altuna

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...]

methylKit: R package for DNA methylation analysis

December 21, 2011 | altuna

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 | altuna

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...]
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