My boss asked me to make a nice slide for a presentation showing the collaborations between researchers at our institute. I have a mountain of other work to do, so in the name of procrastination I spent the afternoon playing with the igraph R library:
click for big image
Code
ChIPpeaksAnnot is a Bioconductor package, built on top of all the Biostrings, BSGenome, IRanges stuff, that will let you annotate peaks with nearby features. Some features (eg. mouse and human TSS positions for current genomes) are made available as data with the package, but it also speaks biomaRt to fetch other features if you need [...]
Crantastic.org – New iusethis / cpanratings type thing for reviewing and rating R CRAN packages. Slightly alarming colours, but potentially useful? Don’t think it includes Bioconductor packages, but source is on Github.
Sometimes I have to make a character vector in R. Say for renaming the columns of a matrix. In which case, I have to laboriously type quotes around each of the names. I know it’s only a minor irritation, but wouldn’t it be nicer if they could be quoted for you? Like in Perl where [...]
Problem:
Dataset 1: ChIPseq-derived transcription factor binding sites. Mouse. Mapped to nearest Ensembl Gene ID,
Dataset 2: Human Illumina Ref6 expression array data (GPL6097, I think) from various cell lines with varying amounts of said transcription factor.
Question:
What are the targets of the transcription factor doing in the expression datasets?
Quick Mapping
As a quick approximation, map the Illumina human [...]