[BioC] DAnTE: Statistical Tool using R and R(D)COM

[Ashoka Polpitiya]

Hi,

We recently released DAnTE (Data Analysis Tool Extension) a
statistical tool with a GUI for the analysis of proteomics and
genomics data under Apache license and thought the folks here would be
interested.

It is based on R and R(D)COM. GUI is written in C# and .NET. I am
thankful to the various R mailing lists for the kind of information I
got. The tool along with an example dataset with instructions on how
to perform a series of analysis steps is available
at http://omics.pnl.gov/software/DAnTE.php (Note: thoroughly tested on
R 2.6.2).

An application note on the tool is recently published in the
Bioinformatics journal:
"DAnTE:  a statistical tool for quantitative analysis of-omics data" -
Polpitiya, Ashoka; Qian, Weijun; Jaitly, Navdeep; Petyuk, Vladislav;
Adkins, Joshua; Camp, David G.; Anderson, Gordon; Smith, Richard,
Bioinformatics 24(3):1556-1558.

Brief abstract:
Data Analysis Tool Extension (DAnTE) is a statistical tool designed to
address challenges associated with quantitative bottom-up, shotgun
proteomics data. This tool has also been demonstrated for microarray
data and can easily be extended to other high-throughput data types.
DAnTE features selected normalization methods, missing value
imputation algorithms, peptide-to-protein rollup methods, an extensive
array of plotting functions and a comprehensive hypothesis-testing
scheme that can handle unbalanced data and random effects. The
graphical user interface (GUI) is designed to be very intuitive and
user friendly.

Thanks again for the great work by the R, R(D)COM and Bioconductor community.

Ashoka Polpitiya
---
Scientist
Pacific Northwest National Laboratory
Richland, WA, USA.