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Road2R
A curated list of amazingly awesome R libraries, resources and package collection.
https://github.com/Ronlee12355/Road2R
Last synced: 4 days ago
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Table of Contents
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Data manipulation
- tibble - efficient display structure for tabular data.
- dbplyr - A 'dplyr' Back End for Databases.
- plyr - the split-apply-combine paradigm for R.
- tidyr - Easily Tidy Data with 'spread()' and 'gather()' Functions.
- stringr - Simple, Consistent Wrappers for Common String Operations.
- jsonlite - A Robust, High Performance JSON Parser and Generator for R.
- Matrix - Sparse and Dense Matrix Classes and Methods.
- xts - tools for time series based data.
- rlist - A Toolbox for Non-Tabular Data Manipulation.
- lobstr - lobstr provides tools in the same vein as str(), which allow you to dig into the detail of an object.
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Network graph
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Visualization
- ggforce - Accelerating 'ggplot2'.
- ggpubr - ''ggplot2'' Based Publication Ready Plots.
- gplots - Various R Programming Tools for Plotting Data.
- rpart.plot - Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'.
- pROC - Display and Analyze ROC Curves.
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Import Data
- DBI - R Database Interface
- RCurl - General Network (HTTP/FTP/...) Client Interface for R.
- data.table - Extension of "data.frame".
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Shiny
- shiny.io - Share your Shiny Applications Online.
- Shiny Developer Conference - Shiny Developer Conference.
- Mastering Shiny - Mastering Shiny: a book.
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Interactive Graphics
- htmlwidgets - framework for creating JavaScript widgets with R.
- plotly - Interactive plots.
- Highcharter - Interactive Highcharts plots.
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Word cloud
- wordcloud - Word Clouds.
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Text mining
- tm - Text Mining Package.
- NLP - Natural Language Processing Infrastructure.
- janeaustenr - Jane Austen's Complete Novels.
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Machine learning
- glmnet - Lasso and Elastic-Net Regularized Generalized Linear Models.
- car - Companion to Applied Regression.
- randomForest - Breiman and Cutler's Random Forests for Classification and Regression.
- boot - Bootstrap Functions (Originally by Angelo Canty for S).
- nnet - Feed-Forward Neural Networks and Multinomial Log-Linear Models.
- nnet - Feed-Forward Neural Networks and Multinomial Log-Linear Models.
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Time series
- zoo - S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations).
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Markdown
- rsconnect - Deployment Interface for R Markdown Documents and Shiny Applications.
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Development in R
- Visual Studio Code - Open source code editor.
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Online blogs
- RPubs - Easy web publishing from R.
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Learning materials
- Writing R extension - The online pdf of telling you how to write your own packages.
- Text Mining with R - A Tidy Approach - This is the website for Text Mining with R.
- ggplot2 Doc - Reference of ggplot2.
- Plotly for R - plotly for R.
- Advanced R - Advanced R.
- Advanced R Solutions - Advanced R Solutions.
- bookdown: Authoring Books and Technical - Documents with R Markdown.
- R語言翻轉教室 - 全中文R語言互動式教材.
- Statistical Rethinking with brms ggplot2 and the tidyverse - Statistical Rethinking with brms, ggplot2, and the tidyverse.
- Shiny Tutorial in Chinese - Shiny中文教程.
- R语言教程 - R Tutorial From Peking University (Mandarin Chinese).
- Tidy evaluation - This guide is now superseded by more recent efforts at documenting tidy evaluation in a user-friendly way.
- DIYtranscriptomics - A full course on the analysis of RNA-seq data using R programming environment and the Bioconductor suite of software packages – a versatile and robust collection of tools for bioinformatics, statistics, and plotting.
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Cheatsheet
- RStudio IDE Cheat Sheet - RStudio IDE Cheat Sheet.
- R Markdown Cheat Sheet - R Markdown Cheat Sheet.
- Shiny - Shiny Cheat Sheet.
- Package Development Cheat Sheet - Package Development Cheat Sheet.
- Data Import Cheat Sheet - Data Import Cheat Sheet.
- Data Transformation Cheat Sheet - Data Transformation Cheat Sheet(dplyr).
- Data Visualization Cheat Sheet - Data Visualization Cheat Sheet with ggplot2.
- Apply Functions Cheat Sheet with purrr - Apply Functions Cheat Sheet.
- Deep Learning with Keras Cheat Sheet - Deep Learning with Keras Cheat Sheet.
- Sparklyr Cheat Sheet - Sparklyr Cheat Sheet.
- Work with Strings - Work with Strings Cheat Sheet.
- Dates and times with lubridate - Dates and Times Cheat Sheet.
- Advanced R - Environments, data Structures, Functions, Subsetting and more by Arianne Colton and Sean Chen.
- Caret - Modeling and Machine Learning in R with the caret package by Max Kuhn.
- data.table - Data manipulation with data.table, cheatsheet by Erik Petrovski.
- Base R - Base R.
- cartography - Thematic maps with spatial objects by Timothée Giraud.
- estimatr - Fast, robust estimators for common models.
- eurostat - R tools to access the eurostat database, by rOpenGov.
- h2o - The R interface to h20’s algorithms for big data and parallel computing.
- How big is your graph? - Graph sizing with base R.
- leaflet - Interactive maps in R with leaflet, by Kejia Shi.
- Machine Learning Modelling - A tabular guide to machine learning algorithms in R, by Arnaud Amsellem.
- mlr - The mlr package offers a unified interface to R’s machine learning capabilities.
- nardl - The nardl package estimates the nonlinear cointegrating autoregressive distributed lag model.
- xplain - Explain statistical functions with XML files and xplain.
- Parallel Computation - Parallel computing in R with the parallel, foreach, and future packages. By Ardalan Mirshani.
- quanteda - Quantitative Analysis of Textual Data in R with the quanteda package by Stefan Müller and Kenneth Benoit.
- randomizr - Automate random assignment and sampling with randomizr. By Alex Coppock.
- Regular Expressions - Basics of regular expressions and pattern matching in R by Ian Kopacka.
- Simple Features (sf) - Tools for working with spatial vector data: points, lines, polygons, etc. Cheatsheet by Ryan Garnett.
- sjmisc - dplyr friendly Data and Variable Transformation, by Daniel Lüdecke.
- survminer - Elegant survival plots, by Przemyslaw Biecek.
- Syntax Comparison - Three code styles compared: $, formula, and tidyverse. By Amelia McNamara.
- Teach R - Concise advice on how to teach R or anything else. By Adi Sarid.
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Bioinformatics
- CancerSubtypes - Cancer subtypes identification, validation and visualization based on multiple genomic data sets.
- consensusOV - Gene expression-based subtype classification for high-grade serous ovarian cancer.
- ConsensusClusterPlus - ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking.
- WGCNA - WGCNA: an R package for weighted correlation network analysis.
- ImmuLncRNA - The R package 'ImmulancRNA' contains 3 method which can caculate the tumor purity, partial correlation coefficient and identify the lncRNA-pathway pairs.
- randomForestSRC - R-package for random forest analysis of regression, classification, survival and more.
- superpc - Supervised Principal Components.
- CoxBoost - Cox models by likelihood based boosting for a single survival endpoint or competing risks.
- survivalsvm - Survival Support Vector Analysis.
- GSVA - Gene Set Variation Analysis for microarray and RNA-seq data.
- isomiRseeker - Detect miRNA isoforms from small RNA-seq data.
- glmnet - glmnet: Lasso and Elastic-Net Regularized Generalized Linear Models.
- OmicCircos - an R application and package for generating high-quality circular plots for omics data.
- RTN - RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons.
- RedeR - Interactive visualization and manipulation of nested networks.
- NbClust - NbClust: An R Package for Determining the Relevant Number of Clusters in a Data Set.
- classifyNMIBC - This package implements a Pearson nearest-centroid classifier that assigns class labels to single samples according to the four transcriptomic UROMOL2021 classes of non-muscle-invasive bladder cancer (NMIBC): class 1, class 2a, class 2b and class 3.
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