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Survey on Indian Research Scholars

Survey on Indian Research Scholars

Recently, I have initiated a survey to gather the issues faced by research scholars across India. I have posted the link to this survey in the facebook page titled “Research Scholars of India”. This survey lasted for 10 days (16-26 August 2014). This...
Restriction digestion of eukaryotic genomes in R

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...

ENCODE Transcription factor tracks

I was trying to overlap the differentially methylated CpGs at the transcription factor binding sites for my data. But I am puzzled to see that the ENCODE consortium which has spent huge amount of money on performing experiments and publishing papers, did not pay much...

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...

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...