Blog Archives

writing #rstats bindings for bwa-mem, my notebook.

July 30, 2014
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I wanted to learn how to bind a C library to R, so I've created the following bindings for BWA. My code is available on github at :https://github.com/lindenb/rbwaMost of the C code was inspired from Heng Li's code https://github.com/lh3/bwa/blob/master...

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Parallelizing #RStats using #make

January 30, 2014
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In the current post, I'll show how to use R as the main SHELL of GNU-Make instead of using a classical linux shell like 'bash'. Why would you do this ? awesomeness Make-based workflow management Make-based execution with --jobs. GNU make knows how to ...

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Connecting to a MongoDB database from R using the C API for MongoDB

September 24, 2010
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Today, Neil posted an article titled" Connecting to a MongoDB database from R using Java". In the current post, I'll show how to use the C API for MongoDB to fetch some MongoDB data from R. The code will be somehow similar to my previous post "A stateful C function for R: parsing Fasta sequences".OK, First, let's...

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Connecting to a MongoDB database from R using the C API for MongoDB

September 24, 2010
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Today, Neil posted an article titled" Connecting to a MongoDB database from R using Java". In the current post, I'll show how to use the C API for MongoDB to fetch some MongoDB data from R. The code will be somehow similar to my previous post "A stateful C function for R: parsing Fasta sequences".OK, First, let's...

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A stateful C function for R: parsing Fasta sequences

April 19, 2010
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In the following post, I'll create a C extension for R. This extension will iterate over all the FASTA sequences in a file and will return a pair(name,sequence) for each sequence, that is to say that I won't store all the sequences in memory.The C code...

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A stateful C function for R: parsing Fasta sequences

April 19, 2010
By

In the following post, I'll create a C extension for R. This extension will iterate over all the FASTA sequences in a file and will return a pair(name,sequence) for each sequence, that is to say that I won't store all the sequences in memory.The C code...

Read more »

Object Oriented Programming with R: My notebook

April 14, 2010
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In the following post, I describe how I've used the OOP features of R to create and use the following class hierarchy:Your browser does not support the <CANVAS> element !/* generated with svg2canvas by Pierre Lindenbaum http://plindenbaum.blogspot.com [email protected] */function paint1271278100588(){var canvas=document.getElementById('ctx1271278100588');if (!canvas.getContext) return;var c=

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Object Oriented Programming with R: My notebook

April 14, 2010
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In the following post, I describe how I've used the OOP features of R to create and use the following class hierarchy:Your browser does not support the <CANVAS> element !/* generated with svg2canvas by Pierre Lindenbaum http://plindenbaum.blogspot.com [email protected] */function paint1271278100588(){var canvas=document.getElementById('ctx1271278100588');if (!canvas.getContext) return;var c=

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‘R’ = dna.translate("AGG") . A custom C function for R, My notebook.

March 26, 2010
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In the following post, I will show how I've implemented a custom C function for R. This C function will translate a DNA to a protein. I'm very new to 'R' so feel free to make any comment about the code.C codeThe data in 'R' are stored in an opaque stru...

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‘R’ = dna.translate("AGG") . A custom C function for R, My notebook.

March 26, 2010
By

In the following post, I will show how I've implemented a custom C function for R. This C function will translate a DNA to a protein. I'm very new to 'R' so feel free to make any comment about the code.C codeThe data in 'R' are stored in an opaque stru...

Read more »