DanteR
DanteR is an entirely R-based program that provides a graphical front-end for common data analysis tasks in "omics", with an emphasis on proteomics. It is the successor to DAnTE, providing all of the previous features plus new functionality.
Key features include
- Improved statistical and data manipulation functions, eg Normalization, Protein-Level ANOVA
- Deep, interactive data exploration, eg Row Plotting, Volcano Plots, PCA Plots
- Graphical output allows creation and export of publication-quality figures
- Relationship tracking between datasets using metadata, for example factor information
- Written as a stand-alone R package using RGtk2
- Code is completely modular, so all functions can be used as stand-alone scripts
- Full power of R is always available to the user via the command line
- User written functions and packages can be integrated as add-ons with easily specified dialogs
- Runs on Windows, Linux and Mac OS-X platforms
See the Software Features below for a more complete list of features
What's New in v1.0.1.1
December 20, 2010
- The 1-Click DanteR windows installer is now available - no need for any pre-installation of R, etc
- Updated to R 2.12 and new Gtk library version
- Number formatting is much faster and "NA" display bug fixed
- Fixed nrow(nosib.miss) bug in eigen_norm line 86 (thanks NingQing)
- Fixed row deletion bug
- Fixed data frame log transform attribute loss (thanks Joe)
- Changed tooltip descriptions for Workspace/Session
- Fixed metadata loss in QuantileN and LR
See also the Change Log
Installation Information
There are two methods for installing DanteR
- Automated installation using the DanteR Installer (Windows only)
- This will install the DanteR Launcher, which can then be used to install and run DanteR (see the detailed instructions on the Installation Page).
- Prerequisites: Microsoft .NET Framework 2.0
- Manual installation
- Because DanteR runs on top of R, manual installation involves several steps, outlined on the Installation Page
- See either the:
Instructions for Windows or
Instructions for Macintosh/Linux
Detailed installation instructions are available on the DanteR Installation page. The DanteR help file also includes installation instructions and screenshots. If you have problems with installation, please e-mail John Sandoval or Tom Taverner
| Download Software Tool | DanteR Help File (Powerpoint) | DanteR Help File (PDF) |
| Version | v1.0.1.1 | Requirements | R 2.10 or higher (auto-installed on Windows) GTK+ (auto-installed on Windows) |
| Date Updated | December 20, 2010 | File Size (Software Tool) | 55 MB (ZIP) |
| Registration Required | No | File size (Source Code) | 478 KB (ZIP) |
| Developers | Tom Taverner and Ashoka Polpitiya | ||
| Comments | |||
Software Features
| Supported file formats | Excel, Excel 2007, SQLite DB, Access, CSV, tab-delimited text | Supported locales | US and European delimiters and decimals |
| Data types | Crosstabulated numeric data (peptide intensity, expression ratios, spectral counts, gene expressions) |
Metadata types | Row metadata (proteins, pathways, biological functions) Column metadata/Factors (Experiment categories) |
| Basic data operations | Merge, sort, filter, apply arbitrary R commands | Metadata operations | Define row/column metadata, plot metadata linkages, create/apply aliases |
| Preprocessing | Normalization via eigenvalues, linear regression, LOESS, quantiles | Imputation | KNN, row means, model-based ANOVA, many others |
| Peptide-to-protein rollup | Via medians, means or quantiles | Parametric statistical operations | N-way ANOVA and robust ANOVA, two-factor protein-level ANOVA, Fisher test, model-based imputation/ANOVA |
| Nonparametric statistics | Shapiro-Wilks, Kruskal-Wallis | Other statistical operations | Interactive volcano plots, significance summaries |
| Plotting | Matrix/Scatterplot, 3D plots using RGL, histogram, QQ, boxplots, ellipses, Venn diagram | Data exploration | K-means and hierarchical clustering, pattern search, 2D and 3D PCA plot, dynamic metadata-linked row plotting |
| Addons | Users can include their own R-based addons to the program | Addon dialogs | A simple markup language allows dialogs to be created with no GUI experience |
DanteR Feature Tour
Application window
|
Main graphical user interface for DanteR |
Boxplots
|
Boxplot display of the range of abundance values within each dataset. |
Plot against row means
|
Plot each column of a crosstab against the mean value of each row |
Histogram
|
Histograms |
Volcano Plot
|
Volcano plot |
Q-Q Plot
|
Q-Q Plot to assess normality of a data set |
Clustering Heatmap
|
Heatmap to visualize clustering |
Protein's Peptides, by Dataset
|
Visualize a protein's peptides as a function of dataset |
Acknowledgment
All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, using this text or a similar variant:
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.