Science Hackday at the Guardian offices in London.
From their wiki:
Where will this take place?
London. The Guardian have kindly offered up part of their building to serve as a Venue.
When will it happen?
The weekend of Saturday, June 19th and Sunday, June 20th, 2010.
What’s a Hack Day?
A bunch of geeks get together in the same physical [...]
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.
My notes on the sequence/quality data from Illumina genome analyser.
Phred
Phred is a program that takes the trace files produced by traditional DNA sequencing, calls the bases and assigns a quality value to each called base.
It calculates a score for each base as:
Qphred = -10 x log10(1/$error_prob)
Where $error_prob is the probability of the base call [...]
My notes on how Macs works. Probably riddled with errors – check out the links below for official docs:
Website
Genome Biology Paper
We’ve used ChIP to grab bits of DNA that correspond to the region bound by the transcription factor (or marked by the histone modification, or whatever). So the data looks something like this:
Except that the [...]