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

Software R package for mixed models with single variance component besides residual error, which allows for efficient prediction with unreplicated training data. Makes ridge regression and other kernel methods accessible to plant breeders interested in genomic selection.

Proper citation: ridge regression Best Linear Unbiased Prediction (RRID:SCR_022519) Copy   

•   Source: SciCrunch Registry

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

Software R package to format data, frame column names, provide quick counts of variable combinations and isolate duplicate records, format tabulation results.

Proper citation: janitor (RRID:SCR_022574) Copy   

•   Source: SciCrunch Registry

https://github.com/taiyun/corrplot

Software R package as visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.

Proper citation: Corrplot (RRID:SCR_023081) Copy   

•   Source: SciCrunch Registry

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

Software R package to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. Package implements classic model averaging for given parameter of interest or predicted values, as well as shrinkage version of model averaging parameter estimates or effect sizes. Package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities.

Proper citation: AICcmodavg (RRID:SCR_023299) Copy   

•   Source: SciCrunch Registry

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

Software R package for mapping country data.Enables mapping of country level and gridded user datasets by facilitating joining to modern world maps and offering visualisation options. Country borders are derived from Natural Earth data v 1.4.0.

Proper citation: rworldmap (RRID:SCR_023394) Copy   

•   Source: SciCrunch Registry

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

Software R package that allows for multiple confidence intervals per row, custom fonts for each text element, custom confidence intervals, text mixed with expressions, and more. Advanced Forest Plot using 'grid' graphics. Used to extend the use of forest plots beyond meta analyses.

Proper citation: forestplot (RRID:SCR_023633) Copy   

•   Source: SciCrunch Registry

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

Software R package to create, modify, analyze, and visualize network graph diagrams. Graph and network visualization using tabular data in R.

Proper citation: DiagrammeR (RRID:SCR_023573) Copy   

•   Source: SciCrunch Registry

https://www.rdocumentation.org/packages/randomizeR/versions/3.0.1

Software R package for randomization of clinical trials. Provides sound scientific evidence for choice of randomization procedure, on the basis of well founded criteria. Includes functions for generating randomization sequences from various randomization procedures as well as various issues for assessment of randomization procedures.

Proper citation: randomizeR (RRID:SCR_023568) Copy   

•   Source: SciCrunch Registry

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

Software R package for training and practicing epidemiologists including methods for two-way and multi-way contingency tables.

Proper citation: epitools (RRID:SCR_023896) Copy   

•   Source: SciCrunch Registry

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

Software R package and jamovi module for simplifying agreement and reliability analyses. Functions within this package include simple tests of agreement, agreement analysis for nested and replicate data, and provide robust analyses of reliability.Used for calculating absolute agreement and estimating required sample sizes for studies of absolute agreement.

Proper citation: SimplyAgree (RRID:SCR_023550) Copy   

•   Source: SciCrunch Registry

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

Software R package for extracting results from mixed effect model objects fit with 'lme4' package. Allows construction of prediction intervals efficiently from large scale linear and generalized linear mixed effects models. Used for analyzing mixed effect regression models.

Proper citation: merTools (RRID:SCR_023700) Copy   

•   Source: SciCrunch Registry

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

Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis.

Proper citation: metagear (RRID:SCR_017085) Copy   

•   Source: SciCrunch Registry

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

Software package implementing various statistical procedures used in psychometry.

Proper citation: R package: psy (RRID:SCR_015660) Copy   

•   Source: SciCrunch Registry

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

Software R package to support functions and datasets for Venables and Ripley MASS. Used for statistical and graphical analysis of data.

Proper citation: Modern Applied Statistics with S (RRID:SCR_019125) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/GALLO/vignettes/GALLO.html

Software R package developed for accurate annotation of genes and quantitative trait loci located in regions identified in common genomic analyses performed in livestock, such as Genome Wide Association Studies and transcriptomics using RNA-Sequencing. Allows graphical visualization of gene and QTL annotation results, data comparison among different grouping factors like methods, breeds, tissues, statistical models, studies and QTL enrichment in different livestock species including cattle, pigs, sheep, and chickens.

Proper citation: Genomic Annotation in Livestock for positional candidate LOci (RRID:SCR_019212) Copy   

•   Source: SciCrunch Registry