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https://CRAN.R-project.org/package=caret

Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.

Proper citation: caret (RRID:SCR_021138) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=openxlsx

Software R package to simplify creation of .xlsx files by providing high level interface to writing, styling and editing worksheets.

Proper citation: openxlsx (RRID:SCR_019185) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=meta

Software general R package providing standard methods for meta analysis.

Proper citation: meta (RRID:SCR_019055) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=CCP

Software R package for significance tests for canonical correlation analysis, including asymptotic tests and Monte Carlo method.

Proper citation: CCP (RRID:SCR_021745) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=ggeffects

Software R package to create tidy data frames of marginal effects for ggplot from model outputs. Used to compute marginal effects and adjusted predictions from statistical models and returns result as tidy data frames.

Proper citation: ggeffects (RRID:SCR_022496) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=betareg

Software R package for modeling beta distributed dependent variables, e.g., rates and proportions. In addition to maximum likelihood regression (for both mean and precision of beta distributed response), bias corrected and bias reduced estimation as well as finite mixture models and recursive partitioning for beta regressions are provided.

Proper citation: Betareg (RRID:SCR_022494) Copy   

•   Source: SciCrunch Registry

https://github.com/topepo/caret

Software R package that contains functions for training and plotting classification and regression models. Includes methods for pre-processing training data, calculating variable importance, and model visualizations.

Proper citation: Classification And Regression Training (RRID:SCR_022524) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=simplePHENOTYPES

Software R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in wide range of genetic architectures, including additive, dominance and epistatic models. Used to simulate multiple traits controlled by loci with varying degrees of pleiotropy.

Proper citation: simplePHENOTYPES (RRID:SCR_022523) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ranger/

Software R package as fast implementation of Random Forests for high dimentional data.

Proper citation: ranger (RRID:SCR_022521) Copy   

•   Source: SciCrunch Registry

https://github.com/h2oai/h2o4gpu

Interface to H2O4GPU, collection of GPU solvers for machine learning algorithms.

Proper citation: h2o4gpu (RRID:SCR_022520) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=ggforce

Software R package providing missing functionality to ggplot2 through extension system introduced with ggplot2 v2.0.0.

Proper citation: ggforce (RRID:SCR_022575) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=NMF

Software R package for nonnegative matrix factorization. Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms.

Proper citation: Algorithms and Framework for Nonnegative Matrix Factorization (RRID:SCR_023124) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/rms/

Software R package as collection of functions that assist with streamline modeling. Works with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.

Proper citation: Regression Modeling Strategies (RRID:SCR_023242) Copy   

•   Source: SciCrunch Registry

https://ndphillips.github.io/FFTrees/

Software package as decision algorithms for solving binary classification problems. Faster and more frugal because every node allows making decision. Apart from being faster and requiring less information, FFTs tend to be robust against overfitting, and are easy to interpret, use, and communicate.

Proper citation: FFTrees (RRID:SCR_023359) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/reshape2/index.html

Software R package to flexible rearrange, reshape and aggregate data. Reshape2 is reboot of reshape package.

Proper citation: reshape2 (RRID:SCR_022679) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/Peptides/index.html

Software R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.

Proper citation: Peptides (RRID:SCR_022675) Copy   

•   Source: SciCrunch Registry

https://stringr.tidyverse.org/

Software package to provide set of functions designed to make working with strings easy. Consistent wrappers for common string operations.

Proper citation: stringr (RRID:SCR_022813) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=vcfR

Software R package to read, write, manipulate and analyze variant call format data. Facilitates easy manipulation of variant call format (VCF) data.

Proper citation: vcfR (RRID:SCR_023453) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=irrCAC

Software R package to calculate various chance-corrected agreement coefficients among 2 or more raters. Among CAC coefficients covered are Cohen's kappa, Conger's kappa, Fleiss' kappa, Brennan-Prediger coefficient, Gwet's AC1/AC2 coefficients, and Krippendorff's alpha. Multiple sets of weights are proposed for computing weighted analyses.

Proper citation: Computing Chance Corrected Agreement Coefficients (RRID:SCR_023176) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=irrICC

Software R package to calculate various intraclass correlation coefficients. Used to quantify inter-rater and intra-rater reliability.

Proper citation: Intraclass Correlations for Quantifying Inter Rater Reliability (RRID:SCR_023175) Copy   

•   Source: SciCrunch Registry