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https://cran.r-project.org/src/contrib/Archive/sybil/

A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language.

Proper citation: sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) Copy   

•   Source: SciCrunch Registry

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

R package from CRAN to extract and visualize the results of multivariate data analysis.

Proper citation: factoextra (RRID:SCR_016692) Copy   

•   Source: SciCrunch Registry

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

Software R package to obtain estimated marginal means for linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays.

Proper citation: emmeans (RRID:SCR_018734) Copy   

•   Source: SciCrunch Registry

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

Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries.

Proper citation: ComplexUpset (RRID:SCR_022752) Copy   

•   Source: SciCrunch Registry

https://github.com/JinmiaoChenLab/Rphenograph

Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis.

Proper citation: Rphenograph (RRID:SCR_022603) Copy   

•   Source: SciCrunch Registry

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

Software package to indicate if two groups are significantly different. Used to add significance brackets to ggplots.

Proper citation: ggsignif (RRID:SCR_023047) Copy   

•   Source: SciCrunch Registry

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

Software statistical analysis R package used for easy analysis and visualization of factorial experiments. Provides interface to common analysis techniques, including analysis of variance and mixed effects modeling. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling.

Proper citation: ez (RRID:SCR_020990) Copy   

•   Source: SciCrunch Registry

https://satijalab.org/signac/index.html

Software framework for analysis of single cell chromatin data. Used for analysis, interpretation, and exploration of single cell chromatin datasets including datasets that co-assay DNA accessibility with gene expression, protein abundance, and mitochondrial genotype. Analysis of single-cell chromatin data including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis, and interactive visualization.

Proper citation: Signac (RRID:SCR_021158) Copy   

•   Source: SciCrunch Registry

https://corybrunson.github.io/ggalluvial/

Software tool as ggplot2 extension for alluvial plots. Used to visualize frequency distributions over time or frequency tables involving several categorical variables. Requires user to specify dimensions, either as separate aesthetics or as key-value pairs, relies on separate layers (stats and geoms) to produce strata, alluvia, and alluvial segments called lodes and flows.

Proper citation: ggalluvial (RRID:SCR_021253) 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

http://cran.r-project.org/web/packages/metaMA/

Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes.

Proper citation: metaMA (RRID:SCR_000408) Copy   

•   Source: SciCrunch Registry

https://github.com/facebook/prophet

Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton.

Proper citation: Prophet (RRID:SCR_017083) Copy   

•   Source: SciCrunch Registry

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

Software R package for estimating structural equation models using instrumental variables.

Proper citation: MIIVsem (RRID:SCR_017444) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html

Software package which brings to R color scales. Created for the Python matplotlib library.

Proper citation: viridis (RRID:SCR_016696) Copy   

•   Source: SciCrunch Registry

https://github.com/benmarwick/cvequality

Software R package contains functions to test for significant differences in coefficients of variation among multiple groups of observations.

Proper citation: cvequality (RRID:SCR_019124) Copy   

•   Source: SciCrunch Registry

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

Software R package to run minimum hypergeometric test.

Proper citation: Minimum-Hypergeometric Test (RRID:SCR_018776) Copy   

•   Source: SciCrunch Registry

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

Software R package to simplify creation of .xlsx files by providing high level interface to writing, styling and editing worksheets.

Proper citation: openxlsx (RRID:SCR_019185) Copy   

•   Source: SciCrunch Registry