Read GTF file into R

The Gene Transfer Format (GTF) is a refinement of the General Feature Format (GFF). A GFF file has nine columns: seqname The name of the sequence; must be a chromosome or scaffold. source The program that generated this feature. feature The name of this type of feature, e.g. "CDS", "start_codon", "stop_codon", and "exon" start The...

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Getting started with the OMIM API

Updated 2016 September 15th: I've made this into an R package, which is available at my GitHub repository A short post on utilising the OMIM API via some wrapper functions I wrote in R. A wrapper, as explained in the Wikipedia article, is simply a subroutine that calls another subroutine. If you plan on using...

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Perl and SAM

Lincoln Stein has written a bunch of modules to deal with SAM/BAM files. Check out the CPAN module. If you are having trouble installing Bio::DB::Sam, you may have to recompile SAMTools with the following command: To install the Perl module on a machine where you don't have root access, follow these instructions. Using this module,...

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