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https://rhrv.r-forge.r-project.org/

Software R package for developing heart rate variability analysis. Allows to import data files containing heartbeat positions in broadly used formats; eliminating outliers or spurious points present in time series with unacceptable physiological values; plotting HRV data and performing time domain, frequency domain and nonlinear HRV analysis.

Proper citation: RHRV (RRID:SCR_023329) Copy   

•   Source: SciCrunch Registry
  

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

Software tool bridges in vitro drug screening with in vivo drug and biomarker discovery. Predicts in vivo or cancer patient drug response and biomarkers to enrich for response from cell line screening data. Builds model using ridge regression, and enables biomarker discovery by imputing drug response in large cancer molecular datasets. Enables drug specific biomarker identification by correcting for general level of drug sensitivity shared among the population.

Proper citation: oncoPredict (RRID:SCR_023872) 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
  

http://www.cbs.dtu.dk/biotools/sequenza/

Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.

Proper citation: Sequenza (RRID:SCR_016662) Copy   

•   Source: SciCrunch Registry
  

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

Software tool to provide color schemes for maps and other graphics. R package to create colorful graphs with pre-made color palettes that visualize data.

Proper citation: RColorBrewer (RRID:SCR_016697) Copy   

•   Source: SciCrunch Registry
  

https://www.rdocumentation.org/packages/statmod/versions/1.4.30

SoftwareR package from CRAN for statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.

Proper citation: statmod (RRID:SCR_016698) Copy   

•   Source: SciCrunch Registry
  

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

Software R package from CRAN as a modular leaf ordering methods for dendrogram nodes. Used as sorting methods to improve readability and interpretability of tree structure. Used for comparison of different distance measures or linkage types, identification of tight clusters and outliers, and for coupled heatmap visualization.

Proper citation: dendsort (RRID:SCR_016693) Copy   

•   Source: SciCrunch Registry
  

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

Software tool for working with data frame like objects, both in memory and out of memory. It is a grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges: mutate, select, filer, summerise, arrange.

Proper citation: dplyr (RRID:SCR_016708) Copy   

•   Source: SciCrunch Registry
  

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

Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders.

Proper citation: ANOCVA (RRID:SCR_016719) Copy   

•   Source: SciCrunch Registry
  

https://github.com/cancerit/BRASS

Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements.

Proper citation: BRASS (RRID:SCR_017091) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for easily tidy data with spread and gather functions. Used for simplifying process of creating tidy data.

Proper citation: tidyr (RRID:SCR_017102) Copy   

•   Source: SciCrunch Registry
  

https://github.com/dgrun/RaceID

Algorithm for identification of rare and abundant cell types from single cell transcriptome data. Based on transcript counts obtained with unique molecular identifies. Used for discovering rare cell types and corresponding marker genes in healthy and diseased organs. Operating system Unix/Linux, Mac OS, Windows.

Proper citation: RaceID (RRID:SCR_017045) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/web/packages/gbm/gbm.pdf

Software R package to implement extensions to Freund and Schapire AdaBoost algorithm and Friedman gradient boosting machine. Includes regression methods for least squares, absolute loss, t distribution loss, quantile regression, logistic, multinomial logistic, Poisson, Cox proportional hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and Learning to Rank measures.

Proper citation: GBM R package (RRID:SCR_017301) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for extensive customization of violin plots. Violin plot is combination of box plot and kernel density plot.

Proper citation: vioplot (RRID:SCR_019293) Copy   

•   Source: SciCrunch Registry
  

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

Software R package to draw geographical maps.

Proper citation: maps (RRID:SCR_019296) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for dynamic report generation using Literate Programming techniques. Comprehensive software tool for reproducible research in R.

Proper citation: knitr (RRID:SCR_018533) Copy   

•   Source: SciCrunch Registry
  

https://github.com/hms-dbmi/EHRtemporalVariability

Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users.

Proper citation: EHRtemporalVariability (RRID:SCR_018663) Copy   

•   Source: SciCrunch Registry
  

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

Software R package to import excel files into R. Has no external dependencies for easy installment and use on all operating systems. Designed to work with tabular data.

Proper citation: readxl (RRID:SCR_018083) Copy   

•   Source: SciCrunch Registry
  

https://mc-stan.org/rstanarm/

Software R package for Bayesian applied regression modeling via Stan.

Proper citation: rstanarm (RRID:SCR_024605) Copy   

•   Source: SciCrunch Registry
  

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

Software R package as visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.Used for graphical display of correlation matrix, confidence interval. Contains some algorithms to do matrix reordering. Good at details, including choosing color, text labels, color labels, layout, etc.

Proper citation: corrplot (RRID:SCR_024683) Copy   

•   Source: SciCrunch Registry