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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://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

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/nboley/idr

Software R package to measure reproducibility of findings identified from replicate experiments and to provide highly stable thresholds based on reproducibility.

Proper citation: IDR (RRID:SCR_017237) 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://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/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/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