This package provides a suite of statistics for identifying areas of the genome under selective pressure. See Jacobs, Sluckin and Kivisild (2016) <doi:10.1534/genetics.115.185900>.
CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.
This package provides functionality for creating Quantile-Quantile (QQ) and Probability-Probability (PP) plots with simultaneous testing bands to asses significance of sample deviation from a reference distribution.
This package is an extension to the testthat package that makes it easy to add graphical unit tests. It provides a Shiny application to manage the test cases.
This package provides a dataset with an uneven number of cases in each class is said to be unbalanced. Many models produce a subpar performance on unbalanced datasets.
This package provides functions for numerical analysis and linear algebra, numerical optimization, differential equations, plus some special functions. It uses Matlab function names where appropriate to simplify porting.
Functions and examples are provided for transmission/disequilibrium tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) "Transmission/disequilibrium tests for extended marker haplotypes".
This package provides a bioinformatics library for Rust. This library provides implementations of many algorithms and data structures that are useful for bioinformatics, but also in other fields.
This package provides a bioinformatics library for Rust. This library provides implementations of many algorithms and data structures that are useful for bioinformatics, but also in other fields.
This package provides a bioinformatics library for Rust. This library provides implementations of many algorithms and data structures that are useful for bioinformatics, but also in other fields.
This package provides a bioinformatics library for Rust. This library provides implementations of many algorithms and data structures that are useful for bioinformatics, but also in other fields.
The rfacts package is an R interface to the Fixed and Adaptive Clinical Trial Simulator ('FACTS') on Unix-like systems. It programmatically invokes FACTS to run clinical trial simulations, and it aggregates simulation output data into tidy data frames. These capabilities provide end-to-end automation for large-scale simulation pipelines, and they enhance computational reproducibility. For more information on FACTS itself, please visit <https://www.berryconsultants.com/software/>.
Estimation of both single- and multiple-assignment Regression Discontinuity Designs (RDDs). Provides both parametric (global) and non-parametric (local) estimation choices for both sharp and fuzzy designs, along with power analysis and assumption checks. Introductions to the underlying logic and analysis of RDDs are in Thistlethwaite, D. L., Campbell, D. T. (1960) <doi:10.1037/h0044319> and Lee, D. S., Lemieux, T. (2010) <doi:10.1257/jel.48.2.281>.
Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to download the TabixFile and index (approximately 3.3 Go).
View and analyze data where bunching is expected. Estimate counter- factual distributions. For earnings data, estimate the compensated elasticity of earnings w.r.t. the net-of-tax rate.
Generating multiple binary and normal variables simultaneously given marginal characteristics and association structure based on the methodology proposed by Demirtas and Doganay (2012) <DOI:10.1080/10543406.2010.521874>.
This package provides high-level modeling functions to define and train models using the torch R package. Models include linear, logistic, and multinomial regression as well as multilayer perceptrons.
Implementation of Tobit type I and type II families for censored regression using the mgcv package, based on methods detailed in Woods (2016) <doi:10.1080/01621459.2016.1180986>.
With the development of new cross-cultural methods this package is intended to combine multiple functions automating and simplifying functions providing a unified analysis approach for commonly employed methods.
This package provides functions to generate ensembles of generalized linear models using competing proximal gradients. The optimal sparsity and diversity tuning parameters are selected via an alternating grid search.
It is devoted to Cramer-von Mises goodness-of-fit tests. It implements three statistical methods based on Cramer-von Mises statistics to estimate and test a regression model.
Broken adaptive ridge estimator for censored data is used to select variables and estimate their coefficients in the semi-parametric accelerated failure time model for right-censored survival data.
Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.