Publications by Kalyan Kumar Pasumarthy
Create a GENCODE transcript database in R
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 following information:loads the needs bioconductor packagesgives information about crea...
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CpG Island shelves
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 across a variety of tissues and cell populations (Irizarry 2009, Ziller 2013). It is now proven th...
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Restriction digestion of eukaryotic genomes in R
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 prokaryotic genomes or smaller eukaryotic chromosomes individually. However, no desktop tool or brows...
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methylKit for bisulfite sequencing data analysis
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 bisulfite analysis with clarity. Altuna Akalin, the author of the methylKit has been actively supp...
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Extending methylKit : Extract promoters with differentially methylated CpGs
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 RRBS or WGBS, methylKit does a pretty good job by identifying the differentially methylated ind...
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Extending methylKit: Christmas Offer for Methylome Researchers
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 sequencing data. I also started just like you and spent hours and days learning R/Bioconductor related pac...
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