Brownian motion simulation in R
I have based this post on a very useful piece of code which basically is the core of my own implementation of a Brownian Motion simulation in R. The original reference code [Read more...]
Articles by Benjamin Tovar
Extracting upstream regions of a RefSeq human gene list in R using Bioconductor
Suppose that you want to do local mapping of upstream regions of a given RefSeq IDs in a particular genome in R using Bioconductor. Download the script here.In this case, you may take a look at the Bioconductor AnnotationData Packages here: http:/... [Read more...]
Handling large FASTA sequence datasets in R: Shuffle and retrieve "n" number of sequences of fixed length from the whole FASTA file and export them in a new FASTA file.
When you are working with large FASTA datasets is probable to find out that the sequences are in sort of a mixed quality (obviously, depending on your scientific question),I mean for example, imagine that you retrieve the whole collection of exons of a... [Read more...]
Calculate the average distance between a given DNA motif within DNA sequences in R
Suppose that we want to calculate the expected distance of a DNA motif within a DNA target sequence, if we know the composition bias or the probability distribution (multinomial model) we can compute it just fine.Download the R code [Read more...]
Introduction to Markov Chains and modeling DNA sequences in R
Markov chains are probabilistic models which can be used for the modeling of sequences given a probability distribution and then, they are also very useful for the characterization of certain parts of a DNA or protein string given for example, a bias t... [Read more...]
Generate artificial DNA or protein sequences in R in a single line of code.
To generate an artificial DNA sequence of "n" bases long with a fixed composition bias in just one line of code, just open your R prompt and type:seqX [Read more...]
Epic R is Epic <- Beginners command reference card
This reference card has been written by Tom Short.Click the image to see the R magic:Thank you for your support Tom.Benjamin [Read more...]
Install R 2.15 and further versions in Debian Squeeze
The last Friday, March 30th, the last stable version of R, the version 2.15.0 was released.So, to install it in Debian Squeeze, or in another Distro powered by Debian (I actually use CrunchBang Linux), just follow the same instructions described here f... [Read more...]
UPDATE: Install R 2.14.2 or R 2.15 in Debian Squeeze
Since not so long, I upgraded the version of R that is included in the Debian repositories (2.11.1 in Squeeze) and I was very happy with it since 2010. But there was some packages that I could not install and then, I decided to upgrade R despite ... [Read more...]
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