TAMALg: is the package available?

I’ve received a lot of questions recently about TAMALg availability. Unfortunately, there is only a difficult-to-install package available right now; I sent it to someone recently and they had a terrible time getting it going.
I do describe the algorithm in the supplementary materials to the ENCODE spike-in competition paper (Johnson et al, Genome Research 2008).
I [...]

TAMALPAIS and promoter arrays

TAMALPAIS NimbleGen Promoter Arrays Array Analysis Problems Mark Bieda
I’ve been receiving some questions on TAMALPAIS usage for promoter arrays via email.
On the TAMALPAIS website, I say “Do not use this for promoter arrays.“
This is actually not quite true; there are a limited number of cases in which TAMALPAIS will perform well for promoter arrays. In [...]

TAMALPAIS known limitation: must be by chromosome

TAMALPAIS Mark Bieda
TAMALPAIS KNOWN LIMITATION:
1. The first field of the gff file must be by chromosome; in particular, it probably needs to be like chr1
or like chr1, chrX, chrY, chr20.
Further details:
I suspect (but am not sure) that anything of the form chr(anything) will work. But I am not sure of this. Note that use of [...]

TAMALg and TAMALPAIS: NimbleGen data analysis

Ok, I wanted to write about the relationship between TAMALPAIS and TAMALg.
keywords: Mark Bieda, TAMALPAIS, TAMALg, NimbleGen, ChIP-chip
Background
A major part of my research is developing algorithms and statistical models for analysis of ChIP-chip experiments – specifically those done with NimbleGen arrays.
TAMALPAIS (available here) predicts binding sites from NimbleGen array data and also does some basic [...]

TAMALPAIS: howto open files

key words: TAMALPAIS, NimbleGen, Mark Bieda, ChIP, server
Background:
TAMALPAIS is the webserver that I created to analyze NimbleGen ChIP-chip data (note that it is not for promoter data). You can find it at:
http://chipanalysis.genomecenter.ucdavis.edu/cgi-bin/tamalpais.cgi
I’ve received queries from a number of people on opening files from my TAMALPAIS server.
Some people have trouble opening the files from the TAMALPAIS [...]