Welcome to the TopKLists page!

For multiple ranked input lists (full or partial) representing the same set of N objects, the package TopKLists offers

1. statistical inference on the lengths of informative top-k lists

2. stochastic aggregation of full or partial lists

3. graphical tools for the statistical exploration of input lists, and for the visualization of aggregation results

Results that can be obtained are a sublist of highly conforming objects in a new rank order, an aggregation map of the top-k objects, or a Venn-diagram of the top-k objects. Typical applications are rank-based data integration and meta-analyses.

The latest stable build can be found on CRAN.

You can find the latest news and the project summary page here.

For a detailed description of the functions provided by the package see the reference manual.

When using TopKLists for the first time it is helpful to make use of reproducible examples, which can be found in the Vignette (comprises the modules TopKInference, TopKSpace, TopKGraphics; the graphical user interface TopKListsGUI is described as well).

Comparison of miRNA measurements

website

R code

data

The TopKLists GUI requires the RGtk2 package, which itself requires an installation of GTK+ version 2.8.0, or higher. If you are experiencing problems with RGtk2/GTK+ installation, please see this website for possible solution.

When using TopKLists in your work please cite:

• Schimek, M. G. et al. (2015). TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists. Stat Appl Genet Mol Biol. 2015 Jun;14(3):311-6. doi: 10.1515/sagmb-2014-0093.

When referring to the module TopKInference in your work please cite:

• Hall, P. and Schimek, M. G. (2012). Moderate deviation-based inference for random degeneration in paired rank lists. J. Amer. Statist. Assoc., 107, 661-672.

When referring to the module TopKSpace in your work please cite:

• Lin, S. and Ding, J. (2009). Integration of ranked lists via Cross Entropy Monte Carlo with applications to mRNA and microRNA studies. Biometrics, 65, 9-18.

• Schimek, M. G., Budinska, E., Kugler, K. and Lin, S. (2011). Package "TopKLists" for rank-based genomic data integration. Proceedings of CompBio 2011, 434-440, DOI: 10.2316/P.2011.742-032.
• Schimek, M. G. and Bloice, M. (2012). Modelling the rank order of Web search engine results. In Komarek, A. and Nagy, S. (eds). Proceedings of the 27th International Workshop on Statistical Modelling. (e-book ISBN 978-80-263-0250-6), Vol. 1, 303-308.
• Schimek, M. G., Mysickova, A. and Budinska, E. (2012). An inference and integration approach for the consolidation of ranked lists. Communications in Statistics - Simulation and Computation, 41:7, 1152-1166.