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.

EXTREME
  (4/5)
The software is designed to be fast for motif discovery on large sequence datasets. The methodology is ingenious and well-justified from computational complexity view. I highly recommend people to try the software, although its software usability still needs improvement. Knowledge in command-line and installation is required.
Posted by Ka-Chun Wong on Jan 08, 2015
kmerHMM
  (5/5)
kmerHMM is designed for motif discovery on protein binding microarray (PBM) data. Especially, its multiple motif elucidation ability has been developed to such an extent that ad hoc processing is not needed by using Hidden Markov Model (HMM). I believe the software can be used on other data with sufficient modification. Especially, its methodology is very mature and novel (belief propagation and HMM).
Posted by Ka-Chun Wong on Jan 08, 2015
HOMER
  (4/5)
Homer is one of the best available motif discovery software suite on the internet, especially for next-generation sequencing. I highly recommend it.
Posted by Ka-Chun Wong on Jan 08, 2015
MEME Suite
  (5/5)
The MEME suite for motif discovery and search is the most popular software for motif discovery. Its pattern recognition ability is one of the best tools I have ever seen. I highly recommend the suite. To be fair, I would also like to note the slightly high computational complexity exist in some of the programs (e.g. long running time). The users need to be aware of it.
Posted by Ka-Chun Wong on Jan 08, 2015
Enrichr
  (5/5)
Totally, 48 databases Enrichr can explore are the most distinguishing feature, attracting me to use.
Posted by Gary on Jan 07, 2015
NanoStriDE
  (5/5)
Tried using R to analyze large data set and was finally able to after getting help from biostatistician (she did all the work). Found this software and it made everything so much easier to get the final product.
Posted by Mike on Jan 06, 2015
FACTERA
  (5/5)
very fast, intuitive, and precise tool. optimized for targeted capture data, but performance on RNA-Seq data reasonably good in my hands, though but not tested against other tools. addition of a paired mode (tumor/normal) option would be a nice feature.
Posted by Matt Shirley on Jan 04, 2015
ImmunomeBase
Thank you Bao Wang. I have modified the url.
Posted by Arnaud Desfeux on Jan 29, 2015
polyaPeak
Thank you Florie. I have modified the url.
Posted by Arnaud Desfeux on Jan 29, 2015
DSAP
DSAP is discontinued, website is not working anymore.
Posted by Yih-Shien Chiang on Jan 28, 2015
polyaPeak
broken link for polyaPeak package
Posted by Florie on Jan 25, 2015
ImmunomeBase
Cann't open the URL.
Posted by Bao Wang on Jan 19, 2015
HiCorrector
Thank you, I have removed the duplicate.
Posted by Arnaud Desfeux on Jan 16, 2015
HiCorrector
Already present in the list
Posted by nservant on Jan 16, 2015