R-universe search: exports:refine

Showing 6 of total 6 results (show query)

bioc

GOfuncR:Gene ontology enrichment using FUNC

GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages ('Homo.sapiens' by default); the GO-graph is included in the package and updated regularly (01-May-2021). GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests: (i) the Wilcoxon rank-sum test that is used when genes are ranked, (ii) a binomial test that is used when genes are associated with two counts and (iii) a Chi-square or Fisher's exact test that is used in cases when genes are associated with four counts. To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.

Maintained by Steffi Grote. Last updated 5 months ago.

genesetenrichment go cpp

5.52 score 55 scripts

tesselle

kairos:Analysis of Chronological Patterns from Archaeological Count Data

A toolkit for absolute and relative dating and analysis of chronological patterns. This package includes functions for chronological modeling and dating of archaeological assemblages from count data. It provides methods for matrix seriation. It also allows to compute time point estimates and density estimates of the occupation and duration of an archaeological site.

Maintained by Nicolas Frerebeau. Last updated 25 days ago.

chronology matrix-seriation archaeology archaeological-science

4.66 score 11 scripts 1 dependents

r-forge

sse:Sample Size Estimation

Provides functions to evaluate user-defined power functions for a parameter range, and draws a sensitivity plot. It also provides a resampling procedure for semi-parametric sample size estimation and methods for adding information to a Sweave report.

Maintained by Thomas Fabbro. Last updated 4 years ago.

4.41 score 16 scripts

louisaslett

BrownianMotion:Brownian Motion Simulations

An implementation of algorithms for simulation of (multivariate) Brownian motion trajectories, including simple unconditional simulation, Brownian bridges, as well as layered and localised Brownian motion simulators.

Maintained by Louis Aslett. Last updated 9 months ago.

brownian-motion

1 stars 3.00 score 1 scripts

kkbrum

optrefine:Optimally Refine Strata

Splits initial strata into refined strata that optimize covariate balance. For more information, please email the author for a copy of the accompanying manuscript. To solve the linear program, the 'Gurobi' commercial optimization software is recommended, but not required. The 'gurobi' R package can be installed following the instructions at <https://www.gurobi.com/documentation/9.1/refman/ins_the_r_package.html>.

Maintained by Katherine Brumberg. Last updated 2 years ago.

2 stars 3.00 score 1 scripts

f-rousset

Infusion:Inference Using Simulation

Implements functions for simulation-based inference. In particular, implements functions to perform likelihood inference from data summaries whose distributions are simulated. The package implements more advanced methods than the ones first described in: Rousset, Gouy, Almoyna and Courtiol (2017) <doi:10.1111/1755-0998.12627>.

Maintained by François Rousset. Last updated 6 months ago.

1.18 score 15 scripts