OMICtools is a workflow for genomic, transcriptomic, proteomic, and metabolomic data analysis. All tools have been classified by omic technologies (NGS, microarray, PCR, MS, NMR), applications and analytical steps. Publication: OMICtools: an informative directory for multi-omic data analysis

Posted by KAORU on Apr 27, 2015
Very powerful R package for differential expression analyses. The new implementation, DESeq2, appears to be one of the most relevant approach to identify differentially expressed genes. Cons: As always it requires to use eSet-like classes
Posted by Claudia Armenise Quartz Bio on Apr 22, 2015
A suite offering a lot of tool, especially for ChIP-sequencing (motif detection, peak overlap, QC...)
Posted by Claudia Armenise Quartz Bio on Apr 22, 2015
Very useful to remove adapters in read 3'end, allowing for mismatches due to sequencing errors. Con: python dependencies
Posted by Claudia Armenise Quartz Bio on Apr 22, 2015
The most useful tool to deal with SAM and BAM files... There is a R Bioconductor package interfacing most of the tools (indexing, conversion...)
Posted by Claudia Armenise Quartz Bio on Apr 22, 2015
SNPper is now available again.
Posted by Vincent J Henry on Apr 27, 2015
I have the following list of GOs


When I try to save the graph as an svg file, the term "GO:0006614" is displayed outside the graph. This also happens if I save the graph as a DOT file (the corresponding node will not have any interactions).

When reducing the number of GOs, the problem is solved, but I already reduced the number to just 5 GOs.

I'm using the following code to produce the graph:

svgRes <- getAmigoTree(goIDs=GO.list, color= "#6599FF", filename="filename.svg", picType="svg")

RamiGO version: 1.12.1
R version: 3.1.1

Thank you.
Posted by Unmapped GOs on Apr 27, 2015
Pascal, use "index.html" instead "venny.php".
Posted by oliveros on Apr 26, 2015
Site is giving a 502 Proxy Error after being extremely slow two days ago
Posted by CD on Apr 22, 2015
HTS Mappers
The problem with the link has been solved.
Posted by Vincent J Henry on Apr 21, 2015