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, including the imputation algorithm described in “A statistical framework for protein quantitation in bottom-up MS-based proteomics.” by Karpievitch and Dabney (DOI 10.1093/bioinformatics/btp362).
This version is still made available because it implements the imputation algorithm described above (see “Model Based Filter/Impute/ANOVA” under the Statistics menu).
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| 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 |
All publications that utilize this software should provide appropriate acknowledgement to PNNL and the DanteR publication. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, as shown in the Readme file for the given application or on the website that more fully describes the application.
These programs are primarily designed to run on Windows machines. Please use them at your own risk. This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.
Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy’s Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.
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