:: DESCRIPTION
Breakway is a suite of programs that take aligned genomic data and report structural variation breakpoints.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Clark MJ, Homer N, O’Connor BD, Chen Z, Eskin A, et al. (2010)
U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line.
PLoS Genet 6(1): e1000832. doi:10.1371/journal.pgen.1000832
:: DESCRIPTION
gHKA , msGenomicHKA, is a software for Modified Hudson–Kreitman–Aguadé Test
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hideki Innan
Modified Hudson–Kreitman–Aguadé Test and Two-Dimensional Evaluation of Neutrality Tests
Genetics July 2006 vol. 173 no. 3 1725-1733
:: DESCRIPTION
growthpred predicts the minimum generation time for a bacterial or archaeal organism based on its codon usage bias intensity (CUB). The CUB index is calculated given two input sets of sequences: 1) highly expressed genes 2) other genes. The application runs 1000 bootstraps and outputs the average and the standard deviation of the predictions.
::DEVELOPER
Microbial evolutionary genomics , Institut Pasteur
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Vieira-Silva S, Rocha EPC, 2010
The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics.
PLoS Genet 6(1): e1000808. doi:10.1371/journal.pgen.1000808
:: DESCRIPTION
GCellIQ ( Genomic Cell Image Quantitator ) is user-friendly open-source software package that aims to provide an automated pipeline for processing large volumes of digital images generated from high-content screening (HCS), including those by RNAi or small compound screening. It’s suitable for batch processing large image dataset with little human interference.
::DEVELOPER
TMHRI Center for Bioengineering and Informatics
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Li F, Zhou X, Zhu J, Ma J, Huang X, et al. (2007)
High content image analysis for human H4 neuroglioma cells exposed to CuO nanoparticles.
Bmc Biotechnology 7: p. 66.
:: DESCRIPTION
GeneSplicer is a fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice . Training data sets for human and Arabidopsis thaliana are included.
::DEVELOPER
the Center for Bioinformatics and Computational Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
The GeneSplicer software is OSI Certified Open Source Software.
Citation:
Pertea , X. Lin , S. L. Salzberg . GeneSplicer : a new computational method for splice site prediction . Nucleic Acids Res . 2001 Mar 1;29(5):1185-90 .
:: DESCRIPTION
Correlate is an Excel plug-in for performing an integrative analysis of two genomic data sets.
If two sets of assays (e.g. gene expression and DNA copy number) have been performed on the same set of patient samples then sparse CCA can be used to find a set of variables in assay 1 that is maximally correlated with a set of variables in assay 2.
::DEVELOPER
Sam Gross / Balasubramanian Narasimhan / Robert Tibshirani /Daniela Witten
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
paper: Witten DM, Tibshirani R, and T Hastie (2009) A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 10(3): 515-534
