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hkestler

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>.

Maintained by Hans A. Kestler. Last updated 1 years ago.

3 stars 5.82 score 122 scripts 6 dependents

bioc

methylscaper:Visualization of Methylation Data

methylscaper is an R package for processing and visualizing data jointly profiling methylation and chromatin accessibility (MAPit, NOMe-seq, scNMT-seq, nanoNOMe, etc.). The package supports both single-cell and single-molecule data, and a common interface for jointly visualizing both data types through the generation of ordered representational methylation-state matrices. The Shiny app allows for an interactive seriation process of refinement and re-weighting that optimally orders the cells or DNA molecules to discover methylation patterns and nucleosome positioning.

Maintained by Bacher Rhonda. Last updated 5 months ago.

dnamethylationepigeneticssequencingvisualizationsinglecellnucleosomepositioning

1 stars 4.90 score 3 scripts

cran

CVST:Fast Cross-Validation via Sequential Testing

The fast cross-validation via sequential testing (CVST) procedure is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on linearly increasing subsets of the data. By eliminating under-performing candidates quickly and keeping promising candidates as long as possible, the method speeds up the computation while preserving the capability of a full cross-validation. Additionally to the CVST the package contains an implementation of the ordinary k-fold cross-validation with a flexible and powerful set of helper objects and methods to handle the overall model selection process. The implementations of the Cochran's Q test with permutations and the sequential testing framework of Wald are generic and can therefore also be used in other contexts.

Maintained by Tammo Krueger. Last updated 3 years ago.

3.75 score 3 dependents

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