GrafGen - Classification of Helicobacter Pylori Genomes

To classify Helicobacter pylori genomes according to genetic distance from nine reference populations. The nine reference populations are hpgpAfrica, hpgpAfrica-distant, hpgpAfroamerica, hpgpEuroamerica, hpgpMediterranea, hpgpEurope, hpgpEurasia, hpgpAsia, and hpgpAklavik86-like. The vertex populations are Africa, Europe and Asia.

Last updated 2 months ago

geneticssoftwaregenomeannotationclassificationcpp

4.48 score 2 scripts 156 downloads

REBET - The subREgion-based BurdEn Test (REBET)

There is an increasing focus to investigate the association between rare variants and diseases. The REBET package implements the subREgion-based BurdEn Test which is a powerful burden test that simultaneously identifies susceptibility loci and sub-regions.

Last updated 4 months ago

softwarevariantannotationsnp

4.30 score 2 scripts 228 downloads

SUITOR - Selecting the number of mutational signatures through cross-validation

An unsupervised cross-validation method to select the optimal number of mutational signatures. A data set of mutational counts is split into training and validation data.Signatures are estimated in the training data and then used to predict the mutations in the validation data.

Last updated 5 months ago

geneticssoftwaresomaticmutation

4.00 score 2 scripts 190 downloads

INPower - An R package for computing the number of susceptibility SNPs

An R package for computing the number of susceptibility SNPs and power of future studies

Last updated 5 months ago

snp

3.60 score 1 scripts 272 downloads

samplesizelogisticcasecontrol - Sample Size and Power Calculations for Case-Control Studies

To determine sample size or power for case-control studies to be analyzed using logistic regression.

Last updated 2 years ago

2.00 score 7 scripts 263 downloads

PRIMEplus - Study Design for Immunotherapy Clinical Trials

Perform sample size, power calculation and subsequent analysis for Immuno-oncology (IO) trials composed of responders and non-responders.

Last updated 1 years ago

1.00 score 166 downloads

NegativeControlOutcomeAdjustment - Estimation of Vaccine Efficacy using Negative Control Outcomes

Methods to reduce confounding bias from unmeasured confounders in observational studies of vaccine efficacy using negative control outcomes.

Last updated 2 years ago

1.00 score 727 downloads

DelayedEffect.Design - Sample Size and Power Calculations using the APPLE, SEPPLE, APPLE+ and SEPPLE+ Methods

Provides sample size and power calculations when the treatment time-lag effect is present and the lag duration is either homogeneous across the individual subject, or varies heterogeneously from individual to individual within a certain domain and following a specific pattern. The methods used are described in Xu, Z., Zhen, B., Park, Y., & Zhu, B. (2017) <doi:10.1002/sim.7157>.

Last updated 2 years ago

1.00 score 5 scripts 318 downloads