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ontologyIndex - Reading Ontologies into R

Functions for reading ontologies into R as lists and manipulating sets of ontological terms - 'ontologyX: A suite of R packages for working with ontological data', Greene et al 2017 <doi:10.1093/bioinformatics/btw763>.

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7.40 score 6 stars 26 dependents 479 scripts 1.9k downloads

ontologyPlot - Visualising Sets of Ontological Terms

Create R plots visualising ontological terms and the relationships between them with various graphical options - Greene et al. 2017 <doi:10.1093/bioinformatics/btw763>.

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4.69 score 7 dependents 58 scripts 530 downloads

ontologySimilarity - Calculating Ontological Similarities

Calculate similarity between ontological terms and sets of ontological terms based on term information content and assess statistical significance of similarity in the context of a collection of terms sets - Greene et al. 2017 <doi:10.1093/bioinformatics/btw763>.

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4.14 score 1 dependents 76 scripts 376 downloads

BeviMed - Bayesian Evaluation of Variant Involvement in Mendelian Disease

A fast integrative genetic association test for rare diseases based on a model for disease status given allele counts at rare variant sites. Probability of association, mode of inheritance and probability of pathogenicity for individual variants are all inferred in a Bayesian framework - 'A Fast Association Test for Identifying Pathogenic Variants Involved in Rare Diseases', Greene et al 2017 <doi:10.1016/j.ajhg.2017.05.015>.

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3.56 score 1 stars 24 scripts 703 downloads

IntervalSurgeon - Operating on Integer-Bounded Intervals

Manipulate integer-bounded intervals including finding overlaps, piling and merging.

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2.80 score 1 dependents 21 scripts 172 downloads

SimReg - Similarity Regression

Similarity regression, evaluating the probability of association between sets of ontological terms and binary response vector. A no-association model is compared with one in which the log odds of a true response is linked to the semantic similarity between terms and a latent characteristic ontological profile - 'Phenotype Similarity Regression for Identifying the Genetic Determinants of Rare Diseases', Greene et al 2016 <doi:10.1016/j.ajhg.2016.01.008>.

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2.78 score 7 scripts 162 downloads

paintmap - Plotting Paintmaps

Plots matrices of colours as grids of coloured squares - aka heatmaps, guaranteeing legible row and column names, without transformation of values, without re-ordering rows or columns, and without dendrograms.

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2.38 score 8 dependents 7 scripts 431 downloads

gsEasy - Gene Set Enrichment Analysis in R

R-interface to C++ implementation of the rank/score permutation based GSEA test (Subramanian et al 2005 <doi: 10.1073/pnas.0506580102>).

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2.20 score 1 stars 16 scripts 280 downloads