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| Software | Description | in common.yaml | listed in library() |
|---|---|---|---|
| abind | GNU R package “Combine multi-dimensional arrays” | y | y |
ade4 | GNU R package “Analysis of Ecological Data : Exploratory | y | |
| ape | GNU R package “Analyses of Phylogenetics and Evolution” | y | |
bitops | GNU R package implementing bitwise operations | y | |
| blogdown | Create Blogs and Websites with R Markdown | y | y |
| bookdown | Authoring Books and Technical Documents with R Markdown | y | y |
catools | GNU R package “Tools: moving window statistics, GIF, | y | y |
| car | Companion to Applied Regression | y | y |
| cargo | y | ||
cluster | GNU R package for cluster analysis by Rousseeuw et al | y | |
| colourpicker | A Colour Picker Tool for Shiny and for Selecting Colours in Plots | y | y |
| cowplot | Streamlined Plot Theme and Plot Annotations for 'ggplot2' | y | y |
| curl | A Modern and Flexible Web Client for R | y | y |
data.table | GNU R package “Extension of data.frame” | y | |
dbi | GNU R package “R Database Interface” | ||
| dbplyr | R Database Interface | y | y |
| dendextend | Extending 'dendrogram' Functionality in R | y | |
dichromat | Color schemes for dichromats | y | |
digest | GNU R package “Create Cryptographic Hash Digests of R | y | |
| emmeans | Estimated Marginal Means, aka Least-Squares Means | y | y |
evaluate | GNU R package “Parsing and Evaluation Tools that Provide | y | |
| fivethirtyeight | Data and Code Behind the Stories and Interactives at 'FiveThirtyEight' | y | y |
| forcats | Data and Code Behind the Stories and Interactives at 'FiveThirtyEight' | y | y |
| foreach | Provides Foreach Looping Construct | y | y |
futile.logger | GNU R package “A Logging Utility for R” | y | |
futile.options | GNU R package “Futile options management” | y | |
gdata | GNU R package “Various R Programming Tools for Data | y | |
getopt | GNU R package “C-like getopt behavior.” | ||
| gganimate | A Grammar of Animated Graphics | y | y |
| GGally | Extension to 'ggplot2' | y | y |
| ggExtra | Add Marginal Histograms to 'ggplot2', and More 'ggplot2' Enhancements | y | y |
ggplot2 | GNU R package “An Implementation of the Grammar of | y | |
| ggpubr | 'ggplot2' Based Publication Ready Plots | y | y |
| ggrepel | Automatically Position Non-Overlapping Text Labels with 'ggplot2' | y | y |
| ggsci | Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2' | y | y |
| ggsignif | Significance Brackets for 'ggplot2' | y | y |
| gifski | Highest Quality GIF Encoder | y | y |
| glmnet | Lasso and Elastic-Net Regularized Generalized Linear Models | y | y |
gplots | GNU R package “Various R Programming Tools for Plotting | y | |
| gridSVG | Export 'grid' Graphics as SVG | y | y |
| gt | Build display tables from tabular data with an easy-to-use set of functions | y | |
gtable | GNU R package “Arrange grobs in tables.” | y | |
gtools | GNU R package “Various R Programming Tools” | y | |
| haven | Import and Export 'SPSS', 'Stata' and 'SAS' Files | y | y |
| igraph | Network Analysis and Visualization | y | y |
| interactions | Comprehensive, User-Friendly Toolkit for Probing Interactions | y | y |
| jpeg | Read and write JPEG images | y | y |
labeling | GNU R package “Axis Labeling” | y | |
lambda.r | GNU R package “Modeling Data with Functional Programming” | y | |
lattice | GNU R package “Lattice Graphics” | y | |
| latticeExtra | Extra Graphical Utilities Based on Lattice | y | y |
| leaps | GNU R package “regression subset selection” | y | y |
| libssl-dev | prereq? | y | |
| libcairo2-dev | perreq? | y | |
| libxt-dev | prereq? | y | |
| libgmp10 | prereq? | y | |
| libgmp-dev | prereq? | y | |
| libmpfr6 | prereq? | y | |
| libmpfr-dev | prereq? | y | |
| lme4 | GNU R package for linear mixed effects model fitting | y | y |
| locfit | Local Regression, Likelihood and Density Estimation | y | y |
| lubridate | Make Dealing with Dates a Little Easier | y | y |
matrix | GNU R package of classes for dense and sparse matrices | y | |
matrixstats | R package “Methods that apply to rows and columns of a matrix” | y | |
| mirbase.db | miRBase: the microRNA database | y | |
| mixdist | Finite Mixture Distribution Models | y | y |
| modelr | Modelling Functions that Work with the Pipe | y | y |
| multcomp | Simultaneous Inference in General Parametric Models | y | y |
munsell | GNU R package “Munsell colour system” | y | |
| mvtnorm | Multivariate Normal and t Distributions | y | y |
| network | Classes for Relational Data | y | y |
nlme | GNU R package for (non-)linear mixed effects models | y | |
| nloptr | R Interface to NLopt | y | y |
| ontologyIndex | Functions for Reading Ontologies into R | y | y |
optparse | GNU R package “Command line option parser.” | ||
permute | GNU R package “Functions for Generating Restricted | ||
| pheatmap | Pretty Heatmaps | y | y |
| pbkrtest | Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison | y | y |
| plotly | Create Interactive Web Graphics via 'plotly.js' | y | y |
| plotROC | Generate Useful ROC Curve Charts for Print and Interactive Use | y | y |
| plotrix | GNU R package “Various plotting functions” | y | y |
plyr | GNU R package “Tools for Splitting, Applying and Combining | y | |
| polynom | A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations | y | y |
proto | GNU R package “Prototype object-based programming” | y | y |
| quantmod | Quantitative Financial Modelling Framework | y | y |
| quantreg | Quantile Regression | y | y |
r.methodss3 | GNU R package “Utility function for defining S3 methods” | y | |
rcolorbrewer | GNU R package providing suitable color palettes | y | |
rcpp | GNU R package “Seamless R and C++ Integration” | y | |
rcurl | GNU R package “General Network (HTTP/FTP/…) Client | y | |
relimp | GNU R package “Relative Contribution of Effects in a | y | |
reshape2 | GNU R package “Flexibly Reshape Data: A Reboot of the | y | y |
| reticulate | Interface to 'Python' | y | y |
rggobi | GNU R package for the GGobi data visualization system | y | |
rgl | GNU R package for three-dimensional visualisation using OpenGL | ||
rgtk2 | GNU R binding for Gtk2 | ||
rmpi | GNU R package interfacing MPI libraries for distributed computing | y | |
| RMySQL | Database Interface and 'MySQL' Driver for R | y | y |
| ROCR | Visualizing the Performance of Scoring Classifiers | y | y |
rserve | GNU R Rserve tcp/ip server and sample clients | y | |
| rstatix | Pipe-Friendly Framework for Basic Statistical Tests | y | y |
rsqlite | GNU R package “SQLite Interface for R” | y | |
| rvest | Easily Harvest (Scrape) Web Pages | y | y |
scales | GNU R package “Scale Functions for Visualization” | y | |
scatterplot3d | GNU R package “3D Scatter Plot” | y | y |
| servr | A Simple HTTP Server to Serve Static Files or Dynamic Documents | y | y |
| Seurat | Tools for Single Cell Genomics | y | y |
| shape | Functions for Plotting Graphical Shapes, Colors | y | y |
| shiny | Web Application Framework for R | y | y |
| shinyjs | Easily Improve the User Experience of Your Shiny Apps in Seconds | y | y |
| Signac | A framework for the analysis of single-cell chromatin data | y | |
| sna | Tools for Social Network Analysis | y | y |
sp | GNU R package “Classes and Methods for Spatial Data” | ||
| sqldf | Manipulate R Data Frames Using SQL | y | y |
| statnet.common | Common R Scripts and Utilities Used by the Statnet Project Software | y | y |
stringr | GNU R package “Simple, Consistent Wrappers for Common | y | |
tcltk2 | GNU R package “Tcl/Tk Additions” | y | y |
testthat | GNU R package “Testthat code. Tools to make testing fun | y | |
| tibble | Simple Data Frames | y | y |
| tidyr | Tidy Messy Data | y | y |
| tidyverse | Easily Install and Load the 'Tidyverse' | y | y |
| transformr | Polygon and Path Transformations | y | y |
vegan | GNU R package “Community Ecology Package” | ||
| VennDiagram | Generate High-Resolution Venn and Euler Plots | y | y |
| VGAM | Vector Generalized Linear and Additive Models | y | y |
| vioplot | Violin Plot | y | y |
| xfun | Miscellaneous Functions by 'Yihui Xie' | y | y |
xml | GNU R package “Tools for Parsing and Generating XML Within | y | y |
xtable | GNU R coerce data to LaTeX and HTML tables | y |
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