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

HiTC
  (5/5)
A good tool to explore Hi-C data together with the statistical power of R
Posted by L. Behagle on Sep 06, 2014
PiHelper
  (5/5)
Great tool for drug- and antibody-target information aggregation.
Posted by Scientist on Sep 02, 2014
NetCoffee
  (5/5)
It's the-state-of-the-art algorithm for the multiple network alignment problem. Fast, Scalable, and Accurate!
Posted by Heidi on Aug 13, 2014
g:Profiler
  (5/5)
Functional annotation enrichment analysis is a powerful first step to understanding an interesting list of genes or gene products.

When I do it, I want the tool to have at least these features:
1) Up-to-date GO annotation data, and support as many other databases as possible;
2) Recognizing multiple types of gene or protein identifier, and do the conversion in the background;
3) Comprehensive filter to reduce or organize the hierarchically inter-related terms to minimize redundancy;
4) Good visualization;
5) Fast.

Of about a dozen different tools I have tried, gProfiler is the only one I found satisfying all. Plus, it has an API in R, which is a life-saver.

One thing that could be improved is to include annotation term clustering according to their semantic or functional similarity (you can try DAVID for this).
Posted by xtYaoNYU on Aug 12, 2014
AliView
  (5/5)
My new favourite!
Posted by John L on Aug 10, 2014
MiRPara
  (5/5)
you need to download the UNAFold software separately from
http://mfold.rna.albany.edu/?q=DINAMelt/software
Posted by J on Aug 05, 2014
MicroMUMMIE
  (5/5)
Let's try!
Posted by landiebuku on Aug 04, 2014
Human Splicing Finder
The problem was due to power outage.
The website was restored and function well.
Please, notice that upgrade of this HSF system could be find at: http://www.umd.be/HSF3/
Posted by Vincent J Henry on Sep 23, 2014
isomiRex
Hi,
I try to use isoMIRex and give 4 files to it. I constantly get: http://bioinfo1.uni-plovdiv.bg/isomiRex/output/tmp68879/res.html

Thanks for your help! Bastian
Posted by Bastian Fromm on Sep 23, 2014
Human Splicing Finder
Human splicing finder is not opening.. Please check that home page.. Its urgent..
Posted by jeslin on Sep 22, 2014
Hiclib
When I run the pipeline 01_iterative_mapping.py, there is something wrong. It said
NFO:hiclib.mapping:Parse the second side of the reads from sams-hg19/SRR027956.sra_2.bam
INFO:hiclib.mapping:Parsing SAM files with basename sams-hg19/SRR027956.sra_2.bam, # of reads: 4959266
2014-09-17T12:42:34 fastq-dump.2.3.5 err: unknown while writing file within file system module - unknown system error
'Broken pipe(32)'
2014-09-17T12:42:34 fastq-dump.2.3.5 err: unknown while writing file within file system module - unknown system error
'Broken pipe(32)'
2014-09-17T12:42:34 fastq-dump.2.3.5 err: unknown while writing file within file system module - failed /data2/GLLi/ph
ong/software/mirnylab-hiclib-b360e6e4c2bc/examples/pipeline2014/fastq/SRR027956.sra
2014-09-17T12:42:34 fastq-dump.2.3.5 err: param invalid while writing file within file system module - Bad position fo
r STDIO write 0 instead of 65536
2014-09-17T12:42:34 fastq-dump.2.3.5 err: unknown while writing file within file system module - failed /data2/GLLi/ph
ong/software/mirnylab-hiclib-b360e6e4c2bc/examples/pipeline2014/fastq/SRR027956.sra
2014-09-17T12:42:34 fastq-dump.2.3.5 err: param invalid while writing file within file system module - Bad position fo
r STDIO write 0 instead of 65536

I don't know how to solve the problem.
Posted by Ping Hong on Sep 18, 2014
HBVdb
Every time I try and access the HBVdb database I am getting the following error


"Your connection is not private
Attackers might be trying to steal your information from hbvdb.ibcp.fr (for example, passwords, messages, or credit cards)."

I have tried using three different internet servers but the problem persists. Please tell me how to access HBVdb.
Posted by anuragsankhyan@yahoo.co.in on Sep 17, 2014
AT_CHLORO
AT_CHLORO team have a problem with the server that should be solved soon.
Please use http://at-chloro.prabi.fr/at_chloro/
Posted by Vincent J Henry on Sep 17, 2014
AT_CHLORO
We are not able to open this site (www.grenoble.prabi.fr) since last few days...its saying service temporarily unavailable. E mail me at - panchsheela.2011@gmail.com
Posted by Panchsheela Nogia (BITS Pilani) on Sep 16, 2014