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

CMGRN
  (5/5)
Good
Posted by KAORU on Apr 27, 2015
DESeq
  (4/5)
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
HOMER
  (4/5)
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
cutadapt
  (4/5)
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
SAMtools
  (5/5)
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
SNPper is now available again.
Posted by Vincent J Henry on Apr 27, 2015
RamiGO
I have the following list of GOs

GO:0006613
GO:0006614
GO:0045047
GO:0072599
GO:0000184

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
VENNY
Pascal, use "index.html" instead "venny.php".
Regards,
OLI
Posted by oliveros on Apr 26, 2015
SNPper
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