Rapidminer is a cool toy to play with machine-learning/data-mining algorithms and it can interface with R. However, it was a bit problematic for me to get the R extension working properly on Mac OS X Leopard for R 2.11. Here is what works for me at the... [Read more...]

BEDtools suite provides command-line functionality when dealing with genomic coordinate based operations, such as overlapping bed files or getting coverage of a bed file over a genome (similar, not exactly same, functionality in R is provided by IRange... [Read more...]

rtracklayer package allows you to access most of the UCSC wiggle tracks from R. However, there is another way which might more practical in situations where you need to summarize the wig track scores over a given set of genomic coordinates. Although yo... [Read more...]

There are a couple of options in R, if you want to utilize multiple cores on your machine. These days my favorite is doMC package, which depends on foreach and multicore packages.in the section below squareroot for each number is calculated in parallel... [Read more...]

C/python style option parsing now available in R with "optparse" package. Check the documentation here and see below to see how it worksuser@node002 scripts $ Rscript filter.transcripts.by.ncRNA.R -husage:  usage: filter.transcripts.by.ncRNA.R [op... [Read more...]

In R, you can treat tables (or data.frames as they are called in R) as SQL tables. That means you can query them as you would query a database with SQL commands. This is particularly useful 1) if you know SQL, hahah:)  2) if you have large tabl... [Read more...]

Principal component analysis (PCA) is a mathematical transformation of possibly(correlated) variables into a number of uncorrelated variables called principal components. The resulting components from this transformation is defined in such a way that t... [Read more...]