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Meat consumption leads to Cancer International Agency for Research on Cancer (a unit of World Health Organization) in its press release announced that consuming more meat leads to increased risk to Cancer. The same was published in The Lancet Oncology journal. Here... read more
Create a REFSEQ transcript database

Create a REFSEQ transcript database

Transcript databases (Txdb) in bioconductor are very good annotation packages. These packages help the researchers annotate the genomic regions of interest to multiple genic elements such as exons, introns, UTRs, CDS, genes etc.,. For the human genome bioconductor... read more
methylKit for bisulfite sequencing data analysis

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... read more
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... read more
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... read more

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... read more

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... read more

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... read more