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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   

•   Source: SciCrunch Registry

https://github.com/cwatson/braingraph/

Software R package for performing graph theory analyses of brain MRI data.

Proper citation: brainGraph (RRID:SCR_017260) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software R package for simultaneous inference in general parametric models. Offers interface to perform multiple comparisons in general context. Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models.

Proper citation: multcomp (RRID:SCR_018255) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software package includes tests for trends and change points detection. Used in analysis of environmental data.

Proper citation: trend (RRID:SCR_018658) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/igraph/

Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus.

Proper citation: igraph (RRID:SCR_019225) Copy   

•   Source: SciCrunch Registry

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

Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses.

Proper citation: tidyverse (RRID:SCR_019186) Copy   

•   Source: SciCrunch Registry

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

Software tool as implementation of network based statistics toolbox in R. Includes mixed effects models.

Proper citation: Network-Based R-Statistics (RRID:SCR_019114) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/variancePartition/

Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays.

Proper citation: variancePartition (RRID:SCR_019204) 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://CRAN.R-project.org/package=simr

Software R package for power analysis of generalized linear mixed models by simulation. Used to calculate power for generalised linear mixed models.

Proper citation: SIMR (RRID:SCR_019287) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=gbs2ploidy

Software R package as functions for inference of ploidy from Genotyping By Sequencing data, including function to infer allelic ratios and allelic proportions in Bayesian framework.

Proper citation: gbs2ploidy (RRID:SCR_019290) Copy   

•   Source: SciCrunch Registry

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

Software R package as collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree.

Proper citation: spdep (RRID:SCR_019294) 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

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry