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R 2.10.0 has been released. Get it while it's hot: http://cran.r-project.org/
Abhishek Tiwari and Mr. Gunn liked this
Hadley Wickham has posted plyr '09 workshop material including slides and R scripts: http://had.co.nz/plyr/09-user/
Tom Walsh and Neil Saunders liked this
Am using R to do some clustering using agnes(from cluster package) my input is a dissimilarity table. i would like to attach some labels to the resulting tree. Any ideas about the way to do that?
if you have the original matrix from which you calculated the dissim object (of class dist), then the row names of the original matrix will be carreid over and will show up when you plot the dendrogram. If you don't have the original matrix, just add an attribute called "Labels" to the dissimilarity object
- Rajarshi Guha
Thanks Rajarsh! but it does not seem to do that. Now i have the dissimilarity, what the syntax for adding the labels attribute? i could be getting it wrong
- george
attr(x ,"Labels") <- c('row1', 'row2' .....
- Rajarshi Guha
Fwd: brew: Creating Repetitive Reports Using Templates - http://learnr.wordpress.com/2009... (via http://friendfeed.com/robsyme...)
Tom Walsh, Abhishek Tiwari and Neil Saunders liked this
Fwd: A nice tutorial on #nextgen #genomics sequence analysis using #R package http://htseq.ucr.edu/ (via http://friendfeed.com/walshtp...)
YGC, Stylish Eve, Paul Bacchus and 3 other people liked this
Fwd: A Quick Guide to Teaching R Programming to Computational Biology Students http://www.ploscompbiol.org/article... #rstats (via http://friendfeed.com/yannabr...)
Khader Shameer and Abhishek Tiwari liked this
Do check the supplementary material, very good tutorial out there
- Abhishek Tiwari
Abhishek Tiwari to Abhishek's feed, Python for Bioinformatics, Ruby for Bioinformatics, R for Bioinformatics
txt2re: headache relief for programmers :: regular expression generator via @CameronNeylon - http://txt2re.com/
Tom Walsh and Marcos de Carvalho liked this
Using foreach type iterators in R - http://learnr.wordpress.com/2009...
Neil Saunders, Abhishek Tiwari and Tom Walsh liked this
Hello Guys., Can you suggest me a R package that does Burrow Wheel Transformation of a string?
You mean Burrows-Wheeler, don't you?
- Ruchira S. Datta
Yes.. Ruchira. I'm concerned with Burrows-Wheeler
- Purnachander G
Have any of you guys successfully used RSPerl to pull R functionality into Perl. Ultimately I guess it is more for convenience as you can always pick up R out files, but that seems unnecessarily painful. I have it working in fits and starts, big issues with the RReferences perl module at the moment. Any help much appreciated !
Tom Walsh, Mike Chelen and Yann Abraham liked this
Well there are several not so well publicised bugs in the RReferences Perl module that comes with the latest release v0.92. Comments in the wrong place, calls in methods to overloaded but not defined functions. Not cool.
- Ian Simpson
Haven't used RSPerl, but did try another R-Perl bridge a few years ago. Forget the name, but it was equally bad code quality. Switch to another language and try RSRuby or RPy instead ;-)
- Neil Saunders
Thanks Neil, it's certainly looking that way, now I have my excuse to branch out (excuse the pun !)
- Ian Simpson
I've never managed to get any of the Perl/R interfaces working reliably. I'm generally not bothered about getting R data into a Perl data-structure though, I usually just use Perl for sticking scripts together, so I tend to leave the actual data as RData files. PL/R (http://www.joeconway.com/plr...) looks quite cool (although I haven't tried it) - gives you the ability to...
more...
- Cass Johnston
Hi Cass, thanks for that. Well I have it working, but not very happy with it. I think part of the problem is that it seems to be mainly designed for people to do R->Perl rather than the other way around. I too have been doing it the way you do, but wanted something more satisfying and efficient (maybe I am just asking too much !). I will have a look at PL/R thanks for the spot.
- Ian Simpson
Statistics-R is the dreadful module, the name of which I forgot earlier. Don't go near it! Except to check out the scathing CPAN reviews - http://cpanratings.perl.org/dist....
- Neil Saunders
Indeed, I've already seen the review of it on CPAN..Ouch. It has been picked up unofficially by another coder who has released a new partial version upgrade v0.03 ? , but the phrase "lost cause" might be appropriate here.
- Ian Simpson
Fwd: Stack Overflow flash mob at #oscon. So cool! http://blog.stackoverflow.com/2009... (via http://friendfeed.com/codingh...)
Chris Miller and Frank liked this
Do any packages for DNA sequence assembly are available in Bioconductor?
I don't know of any tools specifically for sequence assembly in BioC but the people who would know live here: https://stat.ethz.ch/mailman... which is a list for BioC handling of sequence data from Solexa/SOLiD/454 etc.
- Daniel Swan
Dear Swan., Thanks for the information. I keep getting in touch with those guys. Regards, Purna
- Purnachander G
from email
Simple Clustering with RSRuby http://rubyforscientificresear...
Deepak Singh and Jan Aerts liked this
The R Journal - http://journal.r-project.org/index... (via http://friendfeed.com/the-lif...)
R and BioConductor Manual - http://faculty.ucr.edu/~tgirke...
george, Jason Tsai, Ola and 2 other people liked this
LinkedIn: Discussion: The R Project for Statistical Computing - http://www.linkedin.com/groupAn...
dK liked this
Using R to query online databases
- Yann Abraham
from Bookmarklet
“Trying out rsruby - bridging ruby with R” - http://friendfeed.com/e...
Chris Miller, Daniel Swan, Rob Syme and Neil Saunders liked this
Do let us know how you find it. I love the idea and see the potential but haven't been able to justify using it in any projects yet.
- Rob Syme
Saw this a while ago but looked inactive; seems to have been updated Feb 2009. Hopefully better than the Perl R wrapper, which basically just ran R externally and tried to parse the output, as I remember.
- Neil Saunders
I've used RSRuby in a few projects and been generally satisfied. It doesn't actually do that much, but it's nice to pull all your methods together into a single script sometimes.
- Chris Miller
“rapache using the R statistical language and the Apache web server http://biostat.mc.vanderbilt.e...” - http://friendfeed.com/e...
Abhishek Tiwari liked this
Inference for R - http://www.decisionsciencenews.com/...
Is this worth checking out? I got some spammy emails from them, which made me hesitant to try it, even though they were offering a free one year trial for academics.
- Chris Miller
If you're tied to Word and liked the idea of Sweave (i.e., R code in LaTeX) documents, this seem like a useful approach
- Rajarshi Guha
If you're tied to Word and liked the idea of Sweave (i.e., R code in LaTeX) documents, this seem like a useful approach
- Rajarshi Guha
R: a language for data analysis and graphics - http://ecow.engr.wisc.edu/cgi-bin...
Anil Thomas liked this
GOSemSim package for calculate semantic similarity of GO terms and gene products. - http://bioconductor.org/package...
Daniel Swan liked this
R gallery: A host of intricate and beautiful plots (with source code) - http://addictedtor.free.fr/graphiq...
Piotr Byzia, YGC, cheran and 2 other people liked this
woo thats great collection
- Abhishek Tiwari
Comparative methods in R hackathon - http://dx.doi.org/10...
Anil Thomas, Neil Saunders and Nakao M. liked this
Elfred Pagan: Data Mining with R: learning by case studies (via delicious) - http://www.liaad.up.pt/~ltorgo...
YGC, Neil Saunders and Rob Syme liked this
SPRINT: A new parallel framework for R - http://www.mailund.dk/index...
A distributed computation environment for R
- Zaki Manian
NYT: Data Analysts Captivated by R’s Power - http://www.nytimes.com/glogin...
YGC, Zaki Manian, Chris Cotsapas and 2 other people liked this
RSeek.org R-project Search Engine - http://rseek.org/
YGC, Salvatore Loguercio, Zaki Manian and 3 other people liked this
I guess most of the people in this room knows about it, hope this helps the others
- Yann Abraham
Programming in R makes serious statistics serious fun - http://greg.weebly.com/1...
YGC liked this
Yes, I saved this link, but forgot to share in the room. Nice.
- Paulo Nuin
Some odd comments creeping into the discussion at the bottom though!
- Daniel Swan
Google Charts from R - http://www.iq.harvard.edu/blog...
YGC and Zaki Manian liked this
Looks like a step down from the R graphics capabilities :-/
- Rajarshi Guha
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