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http://factominer.free.fr/index.html

Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables.

Proper citation: FactoMineR (RRID:SCR_014602) Copy   

•   Source: SciCrunch Registry

http://CRAN.R-project.org/package=lmerTest

Source code of statistical tests for linear mixed effects models as implemented in lme4. The package also provides the calculation of population means for fixed factors with confidence intervals and corresponding plots.

Proper citation: R package: lmerTest (RRID:SCR_015656) 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/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://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://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://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://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://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=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://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=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

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://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://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://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