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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.

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geneticssoftwaresomaticmutation

4.30 score 4 scripts 325 downloads

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.

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geneticssoftwaregenomeannotationclassificationcpp

4.18 score 2 scripts 308 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.

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softwarevariantannotationsnp

4.00 score 3 scripts 408 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

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snp

3.60 score 3 scripts 392 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.

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2.00 score 8 scripts 289 downloads

SATS - Signature Analyzer for Targeted Sequencing (SATS)

Performs mutational signature analysis for tumors profiled by targeted sequencing. Unlike the canonical analysis of mutational signatures, SATS factorizes the mutation count matrix into a panel-context matrix (measuring the number of mutation opportunities per million base pairs for each tumor), a signature profile matrix, and a signature activity matrix. SATS also calculates the expected number of mutations attributed to each signature, namely the signature burden, for each tumor profiled by targeted sequencing. For more details see Lee et al. (2024) <doi:10.1101/2023.05.18.23290188>.

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1.48 score 15 scripts 520 downloads

JPSurv - Joinpoint Model for Relative and Cause-Specific Survival

Contains functions for fitting a joinpoint proportional hazards model to relative survival or cause-specific survival data, including estimates of joinpoint years at which survival trends have changed and trend measures in the hazard and cumulative survival scale. See Yu et al.(2009) <doi:10.1111/j.1467-985X.2009.00580.x>.

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1.30 score 2 stars 1 scripts 363 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.

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1.00 score 205 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.

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1.00 score 1 stars 358 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>.

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1.00 score 5 scripts 236 downloads