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BoolNet - Construction, Simulation and Analysis of Boolean Networks

Functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks <doi:10.1093/bioinformatics/btq124>.

Last updated

5.72 score 3 stars 3 dependents 196 scripts 983 downloads

TunePareto - Multi-Objective Parameter Tuning for Classifiers

Generic methods for parameter tuning of classification algorithms using multiple scoring functions (Muessel et al. (2012), <doi:10.18637/jss.v046.i05>).

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3.14 score 1 stars 2 dependents 38 scripts 331 downloads

geneticumap - Evolutionary Algorithm for UMAP-based Clustering Pipeline Parameter Optimization for Single-Cell RNA-Seq Data

The geneticumap package searches for single-cell clustering parameters by treating the Seurat preprocessing and clustering workflow as an optimization problem. The UMAP-based clustering pipeline parameters for single-cell RNA-seq data (like resolution, number of PCs, or neighbor counts) evolve using an evolutionary algorithm to systematically search for an optimal set of parameters for a given dataset. The most appropriate configuration is objectively identified by the Calinski-Harabasz index. The package is developed at the [Institute of Medical Systems Biology of Ulm University](https://sysbio.uni-ulm.de).

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geneexpressionsinglecelltranscriptomicsclusteringdimensionreductionpreprocessing

3.00 score

BiTrinA - Binarization and Trinarization of One-Dimensional Data

Provides methods for the binarization and trinarization of one-dimensional data and some visualization functions.

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2.53 score 34 scripts 289 downloads

Binarize - Binarization of One-Dimensional Data

Provides methods for the binarization of one-dimensional data and some visualization functions.

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2.48 score 1 stars 9 scripts 369 downloads

GiANT - Gene Set Uncertainty in Enrichment Analysis

Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets, Schmid et al. (2016) <doi:10.1093/bioinformatics/btw030>.

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2.00 score 1 scripts 287 downloads

MOCCA - Multi-Objective Optimization for Collecting Cluster Alternatives

Provides methods to analyze cluster alternatives based on multi-objective optimization of cluster validation indices. For details see Kraus et al. (2011) <doi:10.1007/s00180-011-0244-6>.

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1.85 score 6 scripts 329 downloads