CSZ 1.0 – Characterization of small RNAome for Zebrafish

CSZ 1.0

:: DESCRIPTION

CSZ demonstrats an sRNA class transition from piRNAs to miRNAs as development proceeds.

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 CSZ

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Feb 10;15:117. doi: 10.1186/1471-2164-15-117.
Systematic characterization of small RNAome during zebrafish early developmental stages.
Yao Y, Ma L, Jia Q, Deng W, Liu Z, Zhang Y, Ren J, Xue Y, Jia H1, Yang Q.

ZebIAT 1.0 – Zebrafish Image Analysis Tool

ZebIAT 1.0

:: DESCRIPTION

ZebIAT is a tool for registering zebrafish images acquired by fluorescence microscope as well as differential interference microscope. The tool offers automatic and semi-automatic methods to analyze images and thus allow, e.g. quantitative comparisons between images.

::DEVELOPER

Teppo AnnilaAndre S. Ribeiro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • MatLab

:: DOWNLOAD

 ZebIAT

 :: MORE INFORMATION

Citation:

T. Annila, E. Lihavainen, I.J. Marques, D.R. Williams, O. Yli-Harja and A.S. Ribeiro. 2013.
ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis.
BMC Bioinformatics 2013, 14(Suppl. 10):S5.

RNAmapper v1 – Use of RNA-Seq data to Map and Identify Mutations in Zebrafish

RNAmapper v1

:: DESCRIPTION

RNAmapper uses RNA-seq data to identify both a region of the genome linked to a mutation as well as candidate mutations that may be causal for the phenotype of interest. We have shown that the method can identify mutations that cause nonsense or missense changes to codons, alter transcript splicing, or alter gene expression levels. Here you will find information on how to map your mutations using RNA-Seq data.

::DEVELOPER

Adam Miller, Arish Shah, and Cecilia Moens

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX /Linux
  • R package / Galaxy

:: DOWNLOAD

 RNAmapper

:: MORE INFORMATION

ZFIQ 1.0 – Quantitative Zebrafish Image Analysis

ZFIQ 1.0

:: DESCRIPTION

ZFIQ ( Zebrafish Image Quantitator ) is a user-friendly software package that is designed for quantitative Zebrafish image analysis, whose key features include automated cell detection, segmentation, quantification, and phenotype classification.

::DEVELOPER

TMHRI Center for Bioengineering and Informatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ZFIQ

:: MORE INFORMATION

Citation:

Tianming Liu.
A quantitative zebrafish phenotyping tool for developmental biology and disease modeling.
IEEE Signal and Processing Magazine. 24(1):126-129. 2007