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Road2R

A curated list of amazingly awesome R libraries, resources and package collection.
https://github.com/Ronlee12355/Road2R

Last synced: 10 days ago
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  • Contributing Information

  • 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

    • 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

    • Learning materials

    • 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.
      • 生信爱好者周刊 - 生信爱好者周刊，Weekly of bioinformatics lovers.

    • Shiny

    • 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.
Programming Languages
R 73 C++ 5 JavaScript 4 TeX 2 HTML 2 C 2
Categories
Table of Contents 240 Contributing Information 1
Sub Categories
Bioinformatics 33 Visualization 30 Learning materials 29 Cheatsheet 27 Data manipulation 23 Import Data 18 Shiny 18 Machine learning 15 Single-cell 9 Development in R 9 Interactive Graphics 7 Text mining 5 Time series 5 Online blogs 4 Markdown 3 Network graph 3 Word cloud 2
Keywords
r 45 rstats 13 r-package 10 cran 7 shiny 7 data-science 6 ggplot2 6 machine-learning 4 visualization 4 rcpp 2 api 2 data-visualisation 2 visualisation 2 tidy-data 2 time-series 2 clustering 2 predictive-modeling 2 education 2 classification 2 regression 2 reactive 2 teaching 2 mlr 1 learners 1 imbalance-correction 1 hyperparameters-optimization 1 feature-selection 1 color-palette 1 tidyverse 1 factor 1 texlive 1 latex 1 date-time 1 date 1 fruit 1 bookdown 1 hashmap 1 cplusplus 1 heatmap 1 complex-heatmaps 1 single-cell-analysis 1 microenvironment 1 cell-cell-interaction 1 cell-cell-communication 1 tutorial 1 tuning 1 survival-analysis 1 statistics 1 stacking 1 mlr3 1