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

Software R package for calculating and drawing variable trees. Variable trees display information about nested subsets of data frame.

Proper citation: vtree (RRID:SCR_023458) 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

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

Software R package for analysis of paths from spatial tracking experiments such as Morris water maze and calculation of goal finding strategies. Used for in depth analysis of tracking coordinates from video.

Proper citation: Rtrack (RRID:SCR_023025) Copy   

•   Source: SciCrunch Registry

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

Software R package as set of standards that specify common storage and access model of geographic features made of mostly two dimensional geometries used by geographic information systems. Standardized way to encode spatial vector data. Formalized by Open Geospatial Consortium and International Organization for Standardization.

Proper citation: Simple Features (RRID:SCR_023393) Copy   

•   Source: SciCrunch Registry

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

Software package implements Bayesian multilevel models in R using probabilistic programming language Stan.

Proper citation: brms (RRID:SCR_023862) Copy   

•   Source: SciCrunch Registry

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

Software R package used for searching for optimal clustering procedure for data set.

Proper citation: clusterSim (RRID:SCR_023743) Copy   

•   Source: SciCrunch Registry

https://www.bibliometrix.org/home/

Software R package for comprehensive science mapping analysis. Used for quantitative research in scientometrics and bibliometrics that includes all main bibliometric methods of analysis.

Proper citation: bibliometrix (RRID:SCR_023744) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/DrugSim2DR/

Software R package to predict drug functional similarity to drug repurposing.

Proper citation: DrugSim2DR (RRID:SCR_024564) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/CpGassoc/index.html

Software R package to test association between methylation at CpG sites across genome and phenotype of interest, adjusting for any relevant covariates. Can perform standard analyses of large datasets without need to manually input data. Can handle mixed effects models with chip or batch entering model as random intercept. Includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.

Proper citation: CpGassoc (RRID:SCR_000320) Copy   

•   Source: SciCrunch Registry

https://www.tidyverse.org/blog/2018/11/parsnip-0-0-1/

Software R package to create and manipulate functions commonly used during modeling e.g. fitting the model, making predictions, etc.

Proper citation: Parsnip (RRID:SCR_024744) Copy   

•   Source: SciCrunch Registry

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

Software package provides several scale functions to break down ‘gg’ plot into pieces and align them together with gap plot or without (wrap plot or cut plot) ignoring subplots. Package was first designed to set breakpoints for truncating plot to shrink outlier long branch of phylogenetic tree. Set Axis Break for ggplot2.

Proper citation: ggbreak (RRID:SCR_024824) Copy   

•   Source: SciCrunch Registry

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

Source code for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. It was originally designed for processes observed at arbitrary times in continuous time but some other observation schemes are supported. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time.

Proper citation: MSM (RRID:SCR_015500) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/lme4/index.html

Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue."

Proper citation: lme4 (RRID:SCR_015654) Copy   

•   Source: SciCrunch Registry