Contributing Information

• author's details

Table of Contents

Bioinformatics

• 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.
• CMSclassifier - An R package and an example data set are provided to run the CMSclassifier.
• CMScaller - an R package for consensus molecular subtyping of colorectal cancer pre-clinical models.
• genefu - R package providing various functions relevant for gene expression analysis with emphasis on breast and ovarian cancers.
• ImmuLncRNA - The R package 'ImmulancRNA' contains 3 method which can caculate the tumor purity, partial correlation coefficient and identify the lncRNA-pathway pairs.
• plsRcox - Partial Least Squares Regression for Cox Models and Related Techniques.
• TCGAbiolinks - TCGAbiolinks - An R/Bioconductor package for integrative analysis with TCGA data.
• clusterProfiler - clusterProfiler: an R package for comparing biological themes among gene clusters.
• maftools - maftools - An R package to summarize, analyze and visualize MAF files.
• GCclassifier - GCclassifier: an R package for the prediction of molecular subtypes of gastric cancer.
• immunedeconv - an R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data.
• BLCAsubtyping - Transcriptomic tools to classify bladder tumours according to six published molecular classifications.
• consensusMIBC - This package implements a nearest-centroid transcriptomic classifier, that assigns class labels according to the consensus molecular classification of Muscle-Invasive Bladder Cancer (Manuscript submitted). The consensus classification identifies 6 molecular classes : Luminal Papillary (LumP), Luminal Non Specified (LumNS), Luminal Unstable (LumU), Stroma-rich, Basal/Squamous (Ba/Sq), Neuroendocrine-like (NE-like).
• oncoPredict - Predict Response from Expression Data and Identify Cell line/Clinical Targets and Trends.
• Mime - Mime: A flexible machine-learning framework to construct and visualize models for clinical characteristics prediction and feature selection.
• CoxBoost - Cox models by likelihood based boosting for a single survival endpoint or competing risks.
• plsRcox - Partial Least Squares Regression for Cox Models and Related Techniques.
• cola - cola: A General Framework for Consensus Partitioning.

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 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.
• Dates and times with lubridate - Dates and Times Cheat Sheet.
• Caret - Modeling and Machine Learning in R with the caret package by Max Kuhn.
• Base R - Base R.
• 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.
• mlr - The mlr package offers a unified interface to R’s machine learning capabilities.
• xplain - Explain statistical functions with XML files and xplain.
• 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.
• survminer - Elegant survival plots, by Przemyslaw Biecek.
• Syntax Comparison - Three code styles compared: $, formula, and tidyverse. By Amelia McNamara.
• LaTeX - A reference to the LaTeX typesetting language, useful in combination with knitr and R Markdown.
• Mosaic - The mosaic package is for teaching mathematics, statistics, computation and modeling.
• nardl - The nardl package estimates the nonlinear cointegrating autoregressive distributed lag model.
• Simple Features (sf) - Tools for working with spatial vector data: points, lines, polygons, etc. Cheatsheet by Ryan Garnett.

Data manipulation

• 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.
• lobstr - lobstr provides tools in the same vein as str(), which allow you to dig into the detail of an object.
• 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.
• data.table - Extension of "data.frame".
• reshape2 - Flexibly Reshape Data: A Reboot of the Reshape Package.
• forcats - Tools for Working with Categorical Variables (Factors).
• Matrix - Sparse and Dense Matrix Classes and Methods.
• lubridate - Make Dealing with Dates a Little Easier.
• hashmap - The Faster Hash Map.
• reticulate - Interface to 'Python'.
• moderndive - An R package of datasets and wrapper functions for tidyverse-friendly introductory linear regression.
• xts - tools for time series based data.
• yaml - Methods to Convert R Data to YAML and Back.
• yaml - Methods to Convert R Data to YAML and Back.
• tibble - efficient display structure for tabular data.
• xml2 - Parse XML.
• dplyr - a grammar of data manipulation.

Development in R

• devtools - Tools to Make Developing R Packages Easier.
• Rcpp - Seamless R and C++ Integration.
• testthat - Unit Testing for R.
• bindrcpp - An 'Rcpp' Interface to Active Bindings.
• Visual Studio Code - Open source code editor.
• goodpractice - Advice on R Package Building.
• usethis - Automate Package and Project Setup.
• Anaconda - The World's Most Popular Python/R Data Science Platform.
• roxygen2 - In-Line Documentation for R.

Import Data

• data.table - Extension of "data.frame".
• DBI - R Database Interface
• RCurl - General Network (HTTP/FTP/...) Client Interface for R.
• readr - Read Rectangular Text Data.
• openxlsx - Read, Write and Edit XLSX Files
• readxl - Read Excel Files.
• clipr - Read and Write from the System Clipboard.
• feather - R Bindings to the Feather 'API'.
• haven - Import and Export 'SPSS', 'Stata' and 'SAS' Files.
• httr - Tools for Working with URLs and HTTP.
• DBI - R Database Interface
• git2r - Provides Access to Git Repositories.
• DBI - R Database Interface
• RMySQL - MySQL driver for DBI
• RSQLite - SQlite driver for DBI
• rvest - Easily Harvest (Scrape) Web Pages.
• RCurl - General Network (HTTP/FTP/...) Client Interface for R.
• RCurl - General Network (HTTP/FTP/...) Client Interface for R.

Interactive Graphics

• htmlwidgets - framework for creating JavaScript widgets with R.
• plotly - Interactive plots.
• Highcharter - Interactive Highcharts plots.
• networkD3 - Interative d3 network graphs.
• echarts4r - EChart htmlwidget.
• leaflet - Interactive maps.
• d3heatmap - Interactive d3 heatmaps.

Learning materials

• Writing R extension - The online pdf of telling you how to write your own packages.
• 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.
• 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.
• R Start Here - A guide to some of the most useful R Packages that we know about.
• Efficient R programming - Efficient R programming by Colin Gillespie and Robin Lovelace.
• Machine Learning with TensorFlow(R version) - This repository is for practicing R tensorflow modeling exercises.
• R的极客理想-高级开发篇 - R的极客理想-高级开发篇.
• swirl - swirl is a platform for learning (and teaching) statistics and R simultaneously and interactively.
• stats337 - Stats 337: Readings in Applied Data Science.
• Data Science in Education Book - Book on data science (or data analysis) in education using R.
• datascience-box - Data Science Course in a Box.
• R語言翻轉教室 - 全中文R語言互動式教材.
• DataScienceR - a curated list of R tutorials for Data Science, NLP and Machine Learning.
• MLwR - Machine Learning with R.
• ml-course-r - R code for the assignments of Ng's Coursera machine learning course.
• R Workshops for Beginners - No programming experience required!
• R语言教程 - R Tutorial From Peking University (Mandarin Chinese).
• R語言翻轉教室 - 全中文R語言互動式教材.
• Shiny Tutorial in Chinese - Shiny中文教程.
• ml-course-r - R code for the assignments of Ng's Coursera machine learning course.
• R for Data Science - This is the website for “R for Data Science”.

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.
• xgboost - Extreme Gradient Boosting.
• arules - Mining Association Rules and Frequent Itemsets.
• gbm - gradient boosted regression models.
• neuralnet - Training of Neural Networks.
• mlr - Machine Learning in R.
• ggpomological - Pomological Colors.
• visdat - Preliminary Exploratory Visualisation of Data.
• lares - R Package for Analytics and Machine Learning.
• mlr3 - A clean, object-oriented rewrite of mlr.
• mlrCPO - Composable Preprocessing Operators for MLR.

Markdown

• rsconnect - Deployment Interface for R Markdown Documents and Shiny Applications.
• rmarkdown - Dynamic Documents for R.
• tinytex - tinytex: Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents.

Network graph

• network3D - D3 JavaScript Network Graphs from R.
• snow - Simple Network of Workstations.
• visNetwork - Network Visualization using 'vis.js' Library.

Online blogs

• RPubs - Easy web publishing from R.
• RWeekly - Weekly Updates from the Entire R Community.
• R-bloggers - R news and tutorials contributed by (750) R bloggers.

Shiny

• shiny.io - Share your Shiny Applications Online.
• Mastering Shiny - Mastering Shiny: a book.
• Shiny - Web Application Framework for R.
• shinyAce - Ace editor bindings to enable a rich text editing environment within Shiny.
• shinyBS - Twitter Bootstrap Components for Shiny.
• shinydashboard - Create Dashboards with 'Shiny'.
• ShinyTrials - Shiny applications with shiny & shinydashboard.
• shiny server - Host Shiny applications over the web.
• Awesome Shiny Extensions - Awesome Shiny Extensions.
• shinythemes - Themes for Shiny.
• shiny.semantic - shiny.semantic: Semantic UI Support for Shiny.
• shinymaterial - Implements Material Design in Shiny Applications.
• shinyUIkit - UIkit API for Shiny.
• fullPage - Single page styles for Shiny apps.
• shinybulma - Bulma.io for Shiny.
• shinyMetroUi - Metro 4 UI for Shiny.
• yonder - A reactive web framework built on Shiny with Bootstrap 4.
• gentelellaShiny - Bootstrap 3 Gentelella theme for Shiny dashboards.
• argonDash - Bootstrap 4 Argon template for Shiny dashboards.
• tablerDash - Tabler dashboard template for Shiny with Bootstrap 4.

Single-cell

• Seurat - Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC.
• ccRemover - Removes the Cell-Cycle Effect from Single-Cell RNA-Sequencing Data.
• cellTree - Cell population analysis and visualization from single cell RNA-seq data using a Latent Dirichlet Allocation model.
• SingleR - Reference-Based Single-Cell RNA-Seq Annotation.
• CellChat - CellChat is an R package designed for inference, analysis, and visualization of cell-cell communication from single-cell data. CellChat aims to enable users to identify and interpret cell-cell communication within an easily interpretable framework, with the emphasis of clear, attractive, and interpretable visualizations.
• Harmony - Fast, sensitive and accurate integration of single-cell data with Harmony.
• Signac - Signac is a comprehensive R package for the analysis of single-cell chromatin data. Signac includes functions for quality control, normalization, dimension reduction, clustering, differential activity, and more.
• velocyto - Estimating RNA velocity in single cell RNA sequencing datasets.
• SCpubr - SCpubr provides a streamlined way of generating publication ready plots for known Single-Cell visualizations in a "publication ready" format (SCpubr).

Text mining

• tm - Text Mining Package.