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https://cran.r-project.org/web/packages/rjags/index.html
Software package provides interface from R to JAGS library for Bayesian data analysis. Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
Proper citation: rjags (RRID:SCR_017573) 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
https://CRAN.R-project.org/package=ape
Software R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R.
Proper citation: ape (RRID:SCR_017343) Copy
https://CRAN.R-project.org/package=macc
Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method.
Proper citation: Mediation Analysis of Causality under Confounding (RRID:SCR_017442) Copy
https://cran.r-project.org/web/packages/phangorn/index.html
Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.
Proper citation: Phangorn (RRID:SCR_017302) Copy
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
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://CRAN.R-project.org/package=meta
Software general R package providing standard methods for meta analysis.
Proper citation: meta (RRID:SCR_019055) Copy
http://wbiomed.curtin.edu.au/genepop/
Population genetic data analysis software package. Used to perform exact Hardy Weinberg Equilibrium test. Used for population differentiation and for genotypic disequilibrium among pairs of loci. Computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc. and performs analyses of isolation by distance from pairwise comparisons of individuals or population samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GENEPOP (RRID:SCR_009194) Copy
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
https://github.com/powellgenomicslab/ascend
Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions.
Proper citation: ascend (RRID:SCR_017257) Copy
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
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
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
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