The major new feature in SeqMonk v0.30.x was the introduction of a bridge between SeqMonk and R, which allows the program to transparently run analyses in R from within the SeqMonk interface. This functionality makes it very easy to run popular algorithms such as DESeq and EdgeR without having to write custom scripts or go…
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Fast subset selection by row name in R
Introduction One of the best features about R is the simple way you can use a number of different strategies to create subsets of large data tables. The basic selection mechanisms you have are that you can subset a data frame by providing: A set of column or row indices A set of boolean values…
Generating R reports with vector images from markdown with knitr
Introduction One really nice addition to a standard R environment is the ability to create reports which combine R code, comments and embedded graphical output. The original mechanism for doing this was Sweave, but more recently a second system called knitr has emerged which seems to be more flexible, and this is what I’ve been…