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https://CRAN.R-project.org/package=biomod2

Software R package for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization.

Proper citation: biomod2 (RRID:SCR_018246) Copy   

•   Source: SciCrunch Registry

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

Software R package for fast and accurate precision recall and ROC curve calculations. Calculates accurate precision recall and Receiver Operator Characteristics curves.

Proper citation: precrec (RRID:SCR_018659) Copy   

•   Source: SciCrunch Registry

https://github.com/jkrijthe/Rtsne

Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation.

Proper citation: Rtsne (RRID:SCR_016342) 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

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

Software package provides R interface to NCBI EUtils API, to search databases like GenBank and PubMed, process of those searches. Provides functions that work with NCBI Eutils API to search, download data from, and otherwise interact with NCBI databases.

Proper citation: rentrez (RRID:SCR_021062) Copy   

•   Source: SciCrunch Registry

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

Software python package for reading Portable Encapsulated Projects or PEPs in R.

Proper citation: pepr (RRID:SCR_021077) Copy   

•   Source: SciCrunch Registry

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

Software R package provides alternative canonical correlation,redundancy analysis function, with associated print, plot, and summary methods.

Proper citation: yacca (RRID:SCR_021746) Copy   

•   Source: SciCrunch Registry

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

Software R package for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis.Procedures for Psychological, Psychometric, and Personality Research. Used for personality, psychometric theory and experimental psychology.

Proper citation: psych (RRID:SCR_021744) Copy   

•   Source: SciCrunch Registry

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

Software R package as functions to accompany J. Fox and S. Weisberg R companion to applied regression.

Proper citation: Companion to Applied Regression (RRID:SCR_022137) Copy   

•   Source: SciCrunch Registry

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

Software R package to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Package also provides number of plot and test functions for typical model misspecification problems.

Proper citation: DHARMa (RRID:SCR_022136) Copy   

•   Source: SciCrunch Registry

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

Software R package provides functions for creating and customizing ggplot2 based publication ready plots.Used for creation of ggplot2 based graphs.

Proper citation: ggpubr (RRID:SCR_021139) Copy   

•   Source: SciCrunch Registry

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

Software R package to make surveys processing and analysis easier. Set of functions include interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions.

Proper citation: questionr (RRID:SCR_021379) Copy   

•   Source: SciCrunch Registry

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

Software R package for exploratory data analysis and data visualization for biological sequence, DNA and protein, data.

Proper citation: seqinr (RRID:SCR_022678) Copy   

•   Source: SciCrunch Registry

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

Software R package for taxonomic information from around web. Interacts with suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more.

Proper citation: taxize (RRID:SCR_022677) Copy   

•   Source: SciCrunch Registry

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

Software R package for data analysis, graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, and recoding variables.

Proper citation: Harrell Miscellaneous (RRID:SCR_022497) Copy   

•   Source: SciCrunch Registry

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

Software R package implements large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures.

Proper citation: Bayesian Generalized Linear Regression (RRID:SCR_022522) Copy   

•   Source: SciCrunch Registry

https://academic.oup.com/bioinformatics/article/34/7/1229/4657077

Software R/Shiny application for interactive creation of Circos plot. Used for creation of Circos plot interactively.

Proper citation: shinyCircoss (RRID:SCR_022367) Copy   

•   Source: SciCrunch Registry

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

Software R package for similarity and distance quantification between probability functions. Information Theory and Distance Quantification with R. Provides framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.

Proper citation: philentropy (RRID:SCR_022805) Copy   

•   Source: SciCrunch Registry

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

Software R package for bindings to liblwgeom library.

Proper citation: lwgeom (RRID:SCR_022812) Copy   

•   Source: SciCrunch Registry