Articles by Kalyan Kumar Pasumarthy

Extending methylKit: Christmas Offer for Methylome Researchers

December 16, 2014 | Kalyan Kumar Pasumarthy

Next week is going to be a vacation and most of us are going on vacation. Me too. However, I thought that this Christmas I would OFFER fellow researchers a GOOD SERVICE. Many of the biologists are learning to deal with their high-throughput sequen... [Read more...]

Extending methylKit : Extract promoters with differentially methylated CpGs

October 23, 2014 | Kalyan Kumar Pasumarthy

In my previous post, I wrote about the features of methylKit. Here, I will discuss how to extend bisulfite sequencing data analysis beyond methylKit.Annotation is an important feature of genomic analyses. Coming to bisulfite sequencing analyses such as...

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methylKit for bisulfite sequencing data analysis

October 21, 2014 | Kalyan Kumar Pasumarthy

I have been relying upon methylKit, an R package for my RRBS data analysis. It is one the most highly cited R package for analysing bisulifite sequencing data. It is straight forward to install and it's vignette details all the major steps in the ... [Read more...]

Restriction digestion of eukaryotic genomes in R

April 28, 2014 | Kalyan Kumar Pasumarthy

There are multiple desktop tools (Bioedit, Emboss, various basic bioinformatic tools) and browser based tools (NEBcutter, biotools, In silico restriction digestion and various other tools) available for performing restriction digestion of smaller proka... [Read more...]

CpG Island shelves

March 26, 2014 | Kalyan Kumar Pasumarthy

Nowadays, regions with relatively lower CpG density are gaining importance in DNA methylation studies. This is based on the fact that a majority of CpG rich regions (CpG islands) are non-dynamic and less variant in terms of methylation status probed ac... [Read more...]

Create a GENCODE transcript database in R

February 25, 2014 | Kalyan Kumar Pasumarthy

The following gist will help the researchers in creating the gencode transcript database using the bioconductor packages. I am assuming that the user's computer has preinstalled packages "GenomicRanges" and "GenomicFeatures". Following script has the f... [Read more...]

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Articles by Kalyan Kumar Pasumarthy

Extending methylKit: Christmas Offer for Methylome Researchers

Extending methylKit : Extract promoters with differentially methylated CpGs

methylKit for bisulfite sequencing data analysis

Restriction digestion of eukaryotic genomes in R

CpG Island shelves

Create a GENCODE transcript database in R

Articles by Kalyan Kumar Pasumarthy

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