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>.

Last updated 9 months ago

7.12 score 6 stars 28 packages 276 scripts 1.6k 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>.

Last updated 9 months ago

4.26 score 3 packages 51 scripts 354 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>.

Last updated 7 months ago

4.07 score 1 packages 65 scripts 330 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>.

Last updated 5 months ago

3.41 score 17 scripts 706 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>.

Last updated 9 months ago

2.78 score 6 scripts 195 downloads

IntervalSurgeon - Operating on Integer-Bounded Intervals

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

Last updated 9 months ago

2.73 score 1 packages 18 scripts 281 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.

Last updated 8 years ago

2.08 score 4 packages 6 scripts 198 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>).

Last updated 9 months ago

2.00 score 9 scripts 220 downloads