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

NeurphologyJ
  (5/5)
Dear All,

currently I am applying NeurphologyJ plugin (on ImageJ) in order to measure the projection length in neurons.
I follow the given instructions but in the last step of "Operation Instruction: Neurphology interactive application" I get the follow message "The source stacks must have the same number of images". Also I cannot see the "NeurphologyJHT in options at menu. Thus I cannot complete the analysis.
I am probably missing something or doing wrong.
do you have any ideas what I could do to fix it?

Thank you very much in advance,

Best
Posted by cell lilly on Jul 21, 2015
FancyGene
  (1/5)
This software only displays one gene at a time.

It does not read GFF file format properly. I had to manually alter the features of the GFF file to make it work. Ex. I had to change "five_prime_UTR" to "utr", "CDS" to "exon", "three_prime_UTR" to "utr".

You cannot use any genomic positions greater than 5,000,000 or you get an error
Error: Can't use string ("5000000") as an ARRAY ref while "strict refs" in use at FancyGene/Errors.pm line 218, <fh00001Os_WRKY_genes2.gff3.txt> line 38.

Bug reporting does not work. I tried reporting the bug and I got the following error:
Not Found
The requested URL /~drambald/cgi-bin/fancygene/bugreport.pl was not found on this server.
Apache/2.2.22 (FreeBSD) PHP/5.4.3 proxy_html/3.1.2 mod_ssl/2.2.22 OpenSSL/0.9.8q DAV/2 Server at bio.ieo.eu Port 80
Posted by ken w. on Jul 16, 2015
RefFinder
  (4/5)
As it uses all the 4 software to determine the best reference gene, i would like to know which one among them is the most reliable?
Posted by Newbie on Jul 04, 2015
GenPlay
  (5/5)
Great software

Similar to IGV but much faster and a lot more functions
Posted by Eric on Jun 30, 2015
Path encoding
  (2/5)
This tool is indeed very efficient in compressing fastq files.
Unfortunately in the compressed file you lose all info in the sequence identifier and the quality score.
Posted by Mmoisse on Jun 25, 2015
BioMuta
Today it is not working at all. Please fix it. Thank you.

Sofía
Posted by Sofía Muñoz on Jul 27, 2015
RefFinder
The website does not work anymore, who can process this problem.
Posted by Peter on Jul 26, 2015
VENNY
Unfortunately, the venny page will not load.
Posted by c jaaworski on Jul 24, 2015
PepNovo
It is working now.
Posted by Vincent J Henry on Jul 23, 2015
NeurphologyJ
What's the imageJ version you're using?
NeurphologyJ works with ImageJ 1.43 and we didn't test any newer version.
Posted by Reply to cell lilly on Jul 22, 2015