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https://CRAN.R-project.org/package=shinythemes
Software R package Themes for use with Shiny.
Proper citation: shinythemes (RRID:SCR_022757) Copy
https://CRAN.R-project.org/package=shinyhelper
Software R package to add markdown helpfiles to shiny apps, using modal dialog boxes, with no need to observe each help button separately.
Proper citation: shinyhelper (RRID:SCR_022755) Copy
https://CRAN.R-project.org/package=Rtrack
Software R package for analysis of paths from spatial tracking experiments such as Morris water maze and calculation of goal finding strategies. Used for in depth analysis of tracking coordinates from video.
Proper citation: Rtrack (RRID:SCR_023025) Copy
https://CRAN.R-project.org/package=sf
Software R package as set of standards that specify common storage and access model of geographic features made of mostly two dimensional geometries used by geographic information systems. Standardized way to encode spatial vector data. Formalized by Open Geospatial Consortium and International Organization for Standardization.
Proper citation: Simple Features (RRID:SCR_023393) Copy
https://CRAN.R-project.org/package=ordinal
Software R package implementation of cumulative link models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered logit/probit models.
Proper citation: ordinal (RRID:SCR_022856) Copy
https://CRAN.R-project.org/package=brms
Software package implements Bayesian multilevel models in R using probabilistic programming language Stan.
Proper citation: brms (RRID:SCR_023862) Copy
https://CRAN.R-project.org/package=vtree
Software R package for calculating and drawing variable trees. Variable trees display information about nested subsets of data frame.
Proper citation: vtree (RRID:SCR_023458) Copy
https://CRAN.R-project.org/package=clusterSim
Software R package used for searching for optimal clustering procedure for data set.
Proper citation: clusterSim (RRID:SCR_023743) Copy
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
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
https://cran.r-project.org/web/packages/lattice/index.html
Data visualization software inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs as well as most nonstandard requirements.
Proper citation: R package: lattice (RRID:SCR_015662) Copy
https://cran.r-project.org/web/packages/cowplot/index.html
Software R package as streamlined plot theme and plot annotations for ggplot2. Provides various features that help with creating publication quality figures with ggplot2, such as set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images.
Proper citation: cowplot (RRID:SCR_018081) Copy
https://bioconductor.org/packages/ggtree/
Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.
Proper citation: ggtree (RRID:SCR_018560) Copy
http://cran.r-project.org/web/packages/PSCBS/
Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Proper citation: PSCBS (RRID:SCR_000417) Copy
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
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
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
http://CRAN.R-project.org/package=LMERConvenienceFunctions
Software package that performs backward selection of fixed effects, forward fitting of the random effects, and post-hoc analysis using parallel capabilities. Other functionality includes the computation of ANOVAs with upper- or lower-bound p-values and R-squared values for each model term, model criticism plots, data trimming on model residuals, and data visualization.
Proper citation: R package: LMERConvenienceFunctions (RRID:SCR_015658) Copy
http://jefferis.github.io/nat/
Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures.
Proper citation: NeuroAnatomy Toolbox (RRID:SCR_016716) Copy
https://github.com/cwatson/braingraph/
Software R package for performing graph theory analyses of brain MRI data.
Proper citation: brainGraph (RRID:SCR_017260) Copy
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