OMICtools can help a) experimental researchers/clinicians find appropriate tools for their needs b) developers to stay up to date and to avoid redundancy c) funding agencies to ensure that the submitted projects are high value-added. Do you want help us to improve OMICtools? Call for curators

(Henry et al., 2014) OMICtools: an informative directory for multi-omic data analysis. Database.

OpenMS
  (5/5)
great set of tools with a steep learning curve
Posted by achimt on Nov 20, 2014
LocalAli
  (5/5)
Cool! A multiple local network alignment tool.
Posted by Oliver on Nov 11, 2014
TRAMS
  (2/5)
Pros: Works quite well in Windows but I haven't got it onto our Linux system as our Python isn't new enough.
Cons: It doesn't accept data with INDELs which seems to be a dealbreaker for bacterial projects - though they are less frequent the INDELs are much more likely to result in a phenotype so for us the lack of this sort of annotation means we won't be using it. Pity.
Posted by Richard Haigh on Nov 10, 2014
fastcore
  (5/5)
FASTCORE is available here
http://wwwen.uni.lu/recherche/fstc/life_sciences_research_unit/research_areas/systems_biology/software
Posted by Maria Pires Pacheco on Oct 30, 2014
VENNY
  (5/5)
Very useful tool to obtain a Venn diagram from up to 4 lists
Posted by Sonia on Oct 28, 2014
BEDTools
  (5/5)
Another indispensable tools suite to have, particularly if you work with .bed files, of course !
In comparison, however, Homer is better if you want to intersect further files because it gives more details, ideal to create a Venn diagram !
A big plus of bedtools : tools are very well documented, with schemes ! I like: "shuffle" to randomly relocate peaks, to test significance of a pathway enrichment for example !
Posted by fabien pichon on Oct 27, 2014
RSEM
  (5/5)
Usefull if you want to estimate isoform expression in your RNA-seq. It uses Bowtie by default but you can map with another mapper and just use BAM/SAM file, so RSEM is quite flexible. Routinely used in TCGA workflow, but I would like to highlight that their RSEM UCSC isoforms IDs are sometimes different from Official UCSC isoforms IDs, no idea why...
Posted by Fabien Pichon on Oct 27, 2014
BioVenn
Hello,
you can press 'PNG Only' or 'SVG only' and then use the 'Save As' function in your browser to save the image. More than 3 sets is not possible.
Posted by Tim Hulsen on Nov 21, 2014
BioVenn
Hello,
I can't save the final image. the format php and I can't open it. also is it possible to add more than 3 gene list istead of 3.
Regards
Posted by Reza on Nov 20, 2014
Mauve
The problem has been resolved.
Posted by Vincent J Henry on Nov 20, 2014
Mauve
Mauve URL no longer functions.
Posted by HMorrison on Nov 18, 2014
RFECS
The source code is not available at the official website.
Posted by Ning-Yi SHAO on Nov 11, 2014
MetaboAnalyst
Is your site down right now (11:47 EST)?
Why does your new version not create graphs for metabolite names ending with +, even when I have now added a connecting underscore? I have some duplicate mets from neg and positive mass spec so I have for instance glutamine_+ in my list to differentiate the two.
Posted by Judy on Nov 05, 2014
idTALE
Hi there,
The web app does not work,
We receive the following message:
Network Error (gateway_error)
Posted by OMICtools team on Nov 05, 2014