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Software and Tools

DAnTE

DAnTE helps users to perform various downstream data analysis, data reduction, and data comparison steps. DAnTE includes a graphical environment for visualizing the data during the processing steps. DAnTE can associate one or more "factors" with each dataset, which are then taken into consideration during the data processing. The statistical methods are implemented in R, and the graphical user interface is written in C#, using the R(D)COM server for connectivity.

Features available in DAnTE include:

  • Comprehensive data loading mechanism
    • Tabular data from CSV, Excel files (either abundances or expression ratios)
    • SEQUEST output files for spectral count analysis
  • Diagnostic plots
    • Histograms, boxplots, correlation plots
    • Peptide-protein rollup plots
    • MA plots, PCA plots, etc.
    • Heatmaps with Hierarchical and K-means clustering options
  • Log transformation
  • Rolling up peptides to proteins (3 methods are available)
  • Normalization
    • LOESS normalization
    • Linear Regression Normalization
    • Mean Centering
    • Median Absolute Deviation (MAD) Adjustment across datasets
    • Quantile Normalization
  • Principal Component Analysis
  • Partial Least Squares Analysis
  • ANOVA (multi-way, unbalanced, random effects)
  • Non-parametric tests
  • Save results to a session file (extension .dnt)

Installation Procedure:

DAnTE depends on the following:
  • .NET framework 2.0 (link)
  • R software (version 2.6.0 or higher) and few packages (listed below) (link)
  • R(D)COM application (link to RSrv250_pl1.exe file)
The bundled version (66.9 MB) of the tool includes a setup program that can automatically install these dependancies and a folder containing the R packages required. You can install these packages manually by running R (then menu 'Packages -> Install package(s) from local zip files...') or DAnTE will automatically download and install them when you run DAnTE for the first time (connection to the Internet is required).

Otherwise, you can install them separately following these steps:
  1. Install the .NET framework 2.0 (from Microsoft) if you don't have it already.
  2. Install the R software from R-project.org or from our server: R-2.6.2-win32.exe (30 MB file)
  3. Install the R(D)COM application from the RCom home page or from our server: RSrv250_pl1.exe (3 MB file)
  4. Download DAnTE and install (when you run DAnTE for the first time it will automatically download and install all the required packages)
Download the Bundle Download Software Tool Download Help File Download Source Code

Version v1.0 Requirements R
R(D)COM server
Microsoft .NET Framework 2.0
Date Updated March 31, 2008 File Size (Software Tool) 4.6 MB (ZIP)
Registration Required No File size (Bundle) 67 MB (ZIP)
Developers Ashoka Polpitiya File size (Source Code) 16 MB (ZIP)
Comments The help file is in the Windows compiled help file format (1.7 MB)
There is a tutorial which is a 1.1 MB Powerpoint file
See the complete Revision History for a history of changes
Supplementary Information on running a simple analysis on a sample dataset (1.6 MB)


Note that DAnTE uses the following R packages; these will be automatically downloaded the first time you run DAnTE:

  • amap: Another Multidimensional Analysis Package
  • car: Companion to Applied Regression
  • nlme: Linear and Nonlinear Mixed Effects Models
  • outliers: Tests for outliers
  • fpc: Fixed point clusters, clusterwise regression and discriminant plots
  • pls: Partial Least Squares Regression (PLSR) and Principal Component Regression (PCR)
  • MASS: Main Package of Venables and Ripley's MASS
  • impute: Imputation for microarray data
  • qvalue: Q-value estimation for false discovery rate control
  • e1071: Misc Functions of the Department of Statistics (e1071), TU Wien
  • gplots: Various R programming tools for plotting data
  • ellipse: Functions for drawing ellipses and ellipse-like confidence regions
  • plotrix: Various plotting functions
  • scatterplot3d: 3D Scatter Plot
  • colorspace: Colorspace Manipulation


Acknowledgment

All publications that result from the use of this software should include this statement:

Portions of this research were supported by the National Institute of General Medical Sciences (NIGMS, Large Scale Collaborative Research Grants U54 GM-62119-02), the NIH National Center for Research Resources (RR18522), and the National Institute of Allergy and Infectious Diseases NIH/DHHS (through interagency agreement Y1-AI-4894-01). Work was performed at Pacific Northwest National Laboratory (PNNL) in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research. PNNL is operated by Battelle for the DOE under contract DE-AC05-76RLO-1830.

DAnTE Feature Tour

Application window

DAnTE GUI

 

Correlation Heatmap

Heatmap


 

Boxplots

Boxplots


 

Peptide to Protein Rollup

Rollup Results