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

Open source software package for R programming language that is used to acquire chemical information from online data sources. Package contains functions that allow programmer to interact with webpages and APIs to retrieve chemical information.

Proper citation: webchem (RRID:SCR_017684) Copy   

•   Source: SciCrunch Registry
  

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
  

http://had.co.nz/reshape/

Software R package for flexibly restructuring and aggregating data.

Proper citation: reshape (RRID:SCR_018983) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for perceptual analysis, visualization and organization of spectral colour data. Software framework for parsing, analyzing and organizing colour from spectral data. Used for spectral and spatial analysis of color patterns.

Proper citation: pavo (RRID:SCR_019123) Copy   

•   Source: SciCrunch Registry
  

https://www.rdocumentation.org/packages/pheatmap/versions/0.2/topics/pheatmap

Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters.

Proper citation: pheatmap (RRID:SCR_016418) Copy   

•   Source: SciCrunch Registry
  

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

Software R package to analyze immune cell migration data. Supports pipeline for track analysis by providing methods for data management, quality control, extracting and visualizing migration statistics, clustering tracks, and simulating cell migration.Available measures include displacement, confinement ratio, autocorrelation, straightness, turning angle, and fractal dimension. Measures can be applied to entire tracks, steps, or subtracks with varying length.

Proper citation: celltrackR (RRID:SCR_021021) Copy   

•   Source: SciCrunch Registry
  

https://www.rdocumentation.org/packages/DGCA/versions/1.0.2

Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix.

Proper citation: Differential Gene Correlation Analysis (RRID:SCR_020964) Copy   

•   Source: SciCrunch Registry
  

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

Software package for performing all stages of geometric morphometric shape analysis of landmark points and curves in 2-and-3-dimensions as well as 3D surfaces in the R statistical computing environment.

Proper citation: geomorph (RRID:SCR_016482) Copy   

•   Source: SciCrunch Registry
  

https://bwhbioinfo.shinyapps.io/powerEQTL/

Software R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis.

Proper citation: powereQTL (RRID:SCR_021653) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/SimFFPE/

Software R package to simulate artifact chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissue. Simulates normal reads as well as artifact chimeric reads that are enriched in FFPE samples. These artifact chimeric reads can lead to large amounts of false positive structural variant calls.

Proper citation: SimFFPE (RRID:SCR_021085) Copy   

•   Source: SciCrunch Registry
  

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

Software functional programming tools for R. Used for working with functions and vectors.

Proper citation: purrr (RRID:SCR_021267) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for basic statistical tests including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. Output of each test is automatically transformed into data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate analysis of factorial experiments. Can compute several effect size metrics.Package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.

Proper citation: rstatix (RRID:SCR_021240) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for design and analysis of disease surveillance activities. These functions were originally developed for animal health surveillance activities but can be equally applied to aquatic animal, wildlife, plant and human health surveillance activities. Utilities are included for sample size calculation and analysis of representative surveys for disease freedom, risk-based studies for disease freedom and for prevalence estimation.

Proper citation: RSurveillance (RRID:SCR_021674) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on basis of single or multiple strata of count data presented in contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.

Proper citation: epiR (RRID:SCR_021673) Copy   

•   Source: SciCrunch Registry
  

https://rdrr.io/cran/mvabund/man/mvabund-package.html

Software R package for multivariate microbiome analysis. Statistical methods for analysing multivariate abundance data.

Proper citation: mvabund (RRID:SCR_022713) Copy   

•   Source: SciCrunch Registry
  

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

Software package to generate area proportional Euler diagrams using numerical optimization that display set relationships (intersections, unions, and disjoints) with circles or ellipses. Area Proportional Euler and Venn Diagrams with Ellipses.

Proper citation: eulerr (RRID:SCR_022753) Copy   

•   Source: SciCrunch Registry
  

https://immunarch.com/

Software R package for exploration of single-cell and bulk T-cell/antibody immune repertoires. Framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires.

Proper citation: immunarch (RRID:SCR_023089) Copy   

•   Source: SciCrunch Registry
  

https://CRAN.R-project.org/package=meta4diag

Software R package for bivariate meta analysis of diagnostic test studies using integrated nested Laplace approximation with INLA.

Proper citation: meta4diag (RRID:SCR_023024) Copy   

•   Source: SciCrunch Registry
  

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

Software R package provides quality control and semantic enrichment tools for preparation of health datasets. Enables semantic enrichment of dataset where metavariables are discovered from relationships between input variables determined from user provided ontologies.

Proper citation: eHDprep (RRID:SCR_023401) Copy   

•   Source: SciCrunch Registry