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"package" "repo" "description" "tags"
"1" "Seurat" "CRAN" "single cell omics analysis" "bioinformatics,scRNAseq"
"2" "DESeq2" "BioConductor" "Differential gene expression analysis based on the negative binomial distribution" "bioinformatics,RNAseq"
"3" "dplyr" "CRAN" "Fast data frames manipulation and database query" "wrangling"
"4" "data.table" "CRAN" "Fast data manipulation in a short and flexible syntax" "io,wrangling,data_analysis"
"5" "reshape2" "CRAN" "Flexible rearrange reshape and aggregate data" "wrangling"
"6" "tidyr" "CRAN" "Easily tidy data with spread and gather functions" "wrangling"
"7" "broom" "CRAN" "Convert statistical analysis objects into tidy data frames" "wrangling"
"8" "rlist" "CRAN" "A toolbox for non-tabular data manipulation with lists" "wrangling"
"9" "lubridate" "CRAN" "A set of functions to work with dates and times" "wrangling"
"10" "stringi" "CRAN" "ICU based string processing package" "wrangling"
"11" "stringr" "CRAN" "Consistent API for string processing built on top of stringi" "wrangling"
"12" "bigmemory" "CRAN" "Shared memory and memory-mapped matrices. The big* packages provide additional tools including linear models (biglm) and Random Forests (bigrf)" "data_analysis"
"13" "fuzzyjoin" "CRAN" "Join tables together on inexact matching" "wrangling"
"14" "tidyverse" "CRAN" "Easily install and load packages from the tidyverse" "wrangling"
"15" "snakecase" "CRAN" "Automatically parse and convert strings into cases like snake or camel among others" "wrangling,utility"
"16" "DataExplorer" "CRAN" "Fast exploratory data analysis with minimum code" "exploration,plotting"
"17" "SmartEDA" "CRAN" "data exploration - generate a complete HTML report" "summary"
"18" "tableone" "CRAN" "producing the typical Table 1 (hence the name) from research publications" "summary"
"19" "Hmisc" "CRAN" "functions to describe data as well as utility functions" "exploration,summary,utility"
"20" "sqldf" "CRAN" "Run SQL queries on your data frame" "exploration,data_analysis"
"21" "splitstackshape" "CRAN" "separate columns with multiple comma separated items into new data frame rows" "wrangling"
"22" "validate" "CRAN" "Intuitive data validation based on rules you can define save and re-use" "cleaning"
"23" "paint" "https://milesmcbain.r-universe.dev" "better print methods for dataframe like objects" "data_analysis exploration,summary"
"24" "diffobj" "CRAN" "Diffs for R Objects" "data_analysis exploration"
"25" "dataCompareR" "CRAN" "allows users to compare two datasets and view a report on the similarities and differences" "exploration"
"26" "datapack" "CRAN" "provides an abstraction for collating multiple data objects of different types and metadata describing those objects into a bundle that can be transported and loaded using a single composite file. It is primarily meant as a container to bundle together files for transport to or from DataONE data repositories" "wrangling"
"27" "skimr" "CRAN" "data summary. It is adept at handling both categorical and numeric data" "exploration,summary"
"28" "summarytools" "CRAN" "data summary" "exploration,summary"
"29" "pastecs" "CRAN" "data summary" "time_series,summary"
"30" "psych" "CRAN" "data summary" "exploration,summary"
"31" "hablar" "CRAN" "Simple tools for converting columns to new data types. Intuitive functions for columns with missing values" "wrangling,cleaning"
"32" "janitor" "CRAN" "Simple Tools for Examining and Cleaning Dirty Data" "exploration,wrangling,cleaning"
"33" "outliers" "CRAN" "A collection of some tests commonly used for identifying outliers" "exploration,data_analysis,cleaning"
"34" "frequency" "CRAN" "Generate SPSS/SAS styled frequency tables" "exploration,summary"
"35" "missForest" "CRAN" "The function missForest is used to impute missing values particularly in the case of mixed-type data" "imputation"
"36" "Amelia" "CRAN" "A tool that multiply imputes missing data in a single cross-section (such as a survey) from a time series" "imputation,time_series"
"37" "mice" "CRAN" "Multivariate Imputation by Chained Equations" "imputation"
"38" "VIM" "CRAN" "Visualization and Imputation of Missing Values" "exploration,imputation"
"39" "mi" "CRAN" "Missing Data Imputation and Model Checking" "imputation"
"40" "wrangle" "CRAN" "Supports systematic scrutiny modification and integration of data" "wrangle"
"41" "tibble" "CRAN" "alternative to dataframes used in tidyverse" "wrangle,utility"
"42" "devtools" "CRAN" "various" "development"
"43" "R6" "CRAN" "simpler faster lighter-weight alternative to Rs built-in classes" "dev"
"44" "pryr" "CRAN" "Make it easier to understand whats going on in R" "dev,performance"
"45" "lineprof" "CRAN" "profiling" "development,performance"
"46" "recover" "CRAN" "exception handling" "development"
"47" "git2r" "CRAN" "Gives you programmatic access to Git repositories from R" "development,git"
"48" "usethis" "CRAN" "includes useful functions for any coding project, e.g. update your .Renvironment and .Rprofile files" "development"
"49" "Shiny" "CRAN" "web dashboard" "web,plot"
"50" "flexdashboard" "CRAN" "web dashboard" "web,plot"
"51" "roxygen2" "CRAN" "create documentation" "docs,development"
"52" "staticdocs" "CRAN" "Generate static html documentation for an R package" "docs,development"
"53" "sinew" "CRAN" "Generate roxygen2 skeletons populated with information scraped from the function script" "docs,development"
"54" "arrow" "CRAN" "An interface to the Arrow C++ library" "io"
"55" "fst" "CRAN" "Lightning Fast Serialization of Data Frames for R" "io"
"56" "haven" "CRAN" "Improved methods to import SPSS Stata and SAS files in R" "io"
"57" "jsonlite" "CRAN" "A robust and quick way to parse JSON files in R" "io"
"58" "qs" "CRAN" "Quick serialization of R objects" "io"
"59" "readxl" "CRAN" "Read excel files (.xls and .xlsx) into R" "io"
"60" "openxlsx" "CRAN" "read and write xlsx" "io"
"61" "tidyxl" "CRAN" "import and wrangling" "io"
"62" "readr" "CRAN" "A fast and friendly way to read tabular data into R" "io"
"63" "rio" "CRAN" "A Swiss-Army Knife for Data I/O" "io"
"64" "readODS" "CRAN" "Read OpenDocument Spreadsheets into R as data.frames" "io"
"65" "RcppTOML" "CRAN" "Rcpp Bindings to C++ parser for TOML files" "io"
"66" "vroom" "CRAN" "Fast reading of delimited files" "io"
"67" "writexl" "CRAN" "Portable light-weight data frame to xlsx exporter for R" "io"
"68" "yaml" "CRAN" "R package for converting objects to and from YAML" "io"
"69" "data.table" "CRAN" "parallel table i/o" "io,data_analysis"
"70" "datapasta" "CRAN" "RStudio addins and R functions that make copy-pasting vectors and tables to text painless" "io,utility"
"71" "reticulate" "CRAN" "suite of tools for calling Python from within R as well as translating between R and Python objects such as Pandas data frames and R data frames" "languageAPI,python"
"72" "rpy2" "CRAN" "Python" "languageAPI,python"
"73" "logging" "CRAN" "A logging package emulating the python logging package" "logging,development"
"74" "caret" "CRAN" "Classification and Regression Training" "ML,regression,validation"
"75" "tree" "CRAN" "Title Classification and Regression Trees" "ML,classification,regression,validation"
"76" "e1071" "CRAN" "Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, generalized k-nearest neighbour,more" "ML,regression,classification,bayesian,clustering,validation"
"77" "crossval" "CRAN" "Generic functions for performing cross validation and for computing diagnostic errors" "validation"
"78" "elasticnet" "CRAN" "Elastic-Net for Sparse Estimation and Sparse PCA" "ML"
"79" "tidymodels" "CRAN" "A collection of packages for modeling and statistical analysis that share the underlying design philosophy grammar and data structures of the tidyverse" "ML,regression,utility"
"80" "lme4" "CRAN" "Generalized mixed-effects models" "ML,mixed_models,regression"
"81" "nlme" "CRAN" "Mixed-effects models handling user-specified matrix of residual covariance relevant for the anaysis of repeated observations in longitudinal trials" "ML,mixed_models,regression"
"82" "mlr3" "CRAN" "ML package that supports Object-Oriented programming with R6 objects" "ML,development"
"83" "xgboost" "CRAN" "gradient boosting" "ML"
"84" "forecast" "CRAN" "time series and linear models" "ML,time_series,regression"
"85" "mgcv" "CRAN" "Generalized additive (mixed) models some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood Generalized Cross Validation and similar or using iterated nested Laplace approximation for fully Bayesian inference" "ML,mixed_models,regression"
"86" "zoo" "CRAN" "time series" "ML,time_series"
"87" "igraph" "CRAN" "network analysis" "networks,plot"
"88" "tidygraph" "CRAN" "network manipulation" "networks,plot"
"89" "pacman" "CRAN" "an R package management tool that combines the functionality of base library related functions into intuitively named functions" "package_management"
"90" "renv" "CRAN" "package management" "package_management"
"91" "jetpack" "CRAN" "package management" "package_management"
"92" "parallel" "CRAN" "r base parallelisation library" "parallel"
"93" "foreach" "CRAN" "Executing the loop in parallel" "parallel"
"94" "ddR" "CRAN" "Provides distributed data structures and simplifies distributed computing in R" "parallel"
"95" "foreach" "CRAN" "Executing the loop in parallel" "parallel"
"96" "future" "CRAN" "minimal efficient cross-platform unified Future API for parallel and distributed processing in R" "parallel"
"97" "furrr" "CRAN" "future+purrr" "functional_programming,parallel"
"98" "Rcpp11" "CRAN" "Rcpp provides a powerful API on top of R makes function in R extremely faster. Rcpp11 is a complete redesign of Rcpp targetting C++11" "performance,development"
"99" "compiler" "CRAN" "speeding up your R code using the JIT" "performance,development"
"100" "cpp11" "CRAN" "cpp11 is a header-only R package that helps R package developers handle R objects with C++ code. Similar to Rcpp but with different design trade-offs and features" "performance,development"
"101" "ggplot2" "CRAN" "An implementation of the Grammar of Graphics" "plot"
"102" "ggfortify" "CRAN" "A unified interface to ggplot2 popular statistical packages using one line of code" "plot,statistics"
"103" "ggrepel" "CRAN" "Repel overlapping text labels away from each other" "plot"
"104" "ggalt" "CRAN" "Extra Coordinate Systems Geoms and Statistical Transformations for ggplot2" "plot"
"105" "ggstatsplot" "CRAN" "ggplot2 Based Plots with Statistical Details" "plot,statistics"
"106" "ggtree" "CRAN" "Visualization and annotation of phylogenetic tree" "plot,dendrogram"
"107" "lattice" "CRAN" "A powerful and elegant high-level data visualization system" "plot"
"108" "corrplot" "CRAN" "A graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering" "plot,statistics"
"109" "Cairo" "CRAN" "R graphics device using cairo graphics library for creating high-quality display output" "plot"
"110" "gganimate" "CRAN" "Create easy animations with ggplot2" "plot"
"111" "hrbrthemes" "CRAN" "Opinionated typographic-centric ggplot2 themes and theme components" "plot"
"112" "dendextend" "CRAN" "visualizing adjusting and comparing trees of hierarchical clustering" "plot,dendrogram"
"113" "idendro" "CRAN" "interactive exploration of dendrograms (trees of hierarchical clustering)" "plot,dendrogram"
"114" "patchwork" "CRAN" "Compose several ggplots into panels" "plot"
"115" "ComplexHeatmap" "BioConductor" "provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics" "plot"
"116" "pheatmap" "CRAN" "Pretty heatmaps" "plot"
"117" "eulerr" "CRAN" "Make Euler diagrams - i.e. well-proportioned Venn diagrams" "plot"
"118" "ggthemes" "CRAN" "themes for ggplot2" "plot"
"119" "ggpubr" "CRAN" "publication-ready themes for ggplot2" "plot"
"120" "wesanderson" "CRAN" "Wes Anderson-inspired colour palettes" "plot"
"121" "RColorBrewer" "CRAN" "palettes" "plot"
"122" "ggally" "CRAN" "extends ggplot2 with features to automatically visualise datasets" "plot,exploration"
"123" "plotly" "CRAN" "plotting framework" "plot"
"124" "paletteer" "CRAN" "palettes" "plot"
"125" "ggforce" "CRAN" "extension package for ggplot2" "plot"
"126" "scales" "CRAN" "provides the internal scaling infrastructure used by ggplot2 and gives you tools to override the default breaks labels transformations and palettes" "plot"
"127" "lintr" "CRAN" "linting" "linting,style"
"128" "magrittr" "CRAN" "Let's pipe it" "syntax,pipe"
"129" "pipeR" "CRAN" "Multi-paradigm Pipeline Implementation" "syntax,pipe"
"130" "lambda.r" "CRAN" "Functional programming and simple pattern matching in R" "syntax vectorization,functional_programming"
"131" "purrr" "CRAN" "A FP package for R in the spirit of underscore.js" "syntax,vectorization,functional_programming"
"132" "glue" "CRAN" "Main function glue evaluates variables and R expressions within a quoted string as long as they are enclosed by {} braces. This makes for an elegant paste() replacement" "syntax,utility"
"133" "testthat" "CRAN" "testing" "testing,development"
"134" "covr" "CRAN" "test coverage" "testing,coverage,development"
"135" "XML" "CRAN" "Tools for parsing and generating XML within R" "web,serialization"
"136" "xml2" "CRAN" "Optimized tools for parsing and generating XML within R" "web,serialization"
"137" "httr" "CRAN" "tools for http connections" "web,networking"
"138" "workflowr" "CRAN" "organized + reproducible + shareable data science in R" "workflow,git,markdown,project"
"139" "targets" "CRAN" "pipeline" "workflow,pipeline"
"140" "here" "CRAN" "use paths relative to project root" "workflow"
"141" "rpart" "CRAN" "Recursive partitioning for classification, regression and survival trees" "ML,regression,validation"
"142" "bcv" "CRAN" "R package for performing Bi-Cross-Validation of an SVD" "validation,matrix_factorisation"
"143" "klaR" "CRAN" "Miscellaneous functions for classification and visualization, e.g. regularized discriminant analysis, sknn() kernel-density naive Bayes, an interface to 'svmlight' and stepclass() wrapper variable selection for supervised classification, partimat() visualization of classification rules and shardsplot() of cluster results as well as kmodes() clustering for categorical data, corclust() variable clustering, variable extraction from different variable clustering models and weight of evidence preprocessing" "ML,clustering,classification,bayesian,regression,validation"
"144" "EnsembleCV" "CRAN" "Extensible Package for Cross-Validation-Based Integration of Base Learners" "ML,validation"
"145" "gencve" "CRAN" "General Cross Validation Engine" "ML,validation"
"146" "cvAUC" "CRAN" "Tools for working with and evaluating cross-validated area under the ROC curve (AUC) estimators" "ML,classification,validation"
"147" "CVThresh" "CRAN" "Level-Dependent Cross-Validation Thresholding" "ML,bayesian,validation"
"148" "cvTools" "CRAN" "Tools that allow developers to write functions for cross-validation with minimal programming effort and assist users with model selection." "ML,validation"
"149" "dcv" "CRAN" "Conventional Cross-validation statistics for climate-growth model" "ML,validation"
"150" "cvms" "CRAN" "Cross-Validation for Model Selection " "ML,classification,regression,validation"
"151" "blockCV" "CRAN" "Spatial and Environmental Blocking for K-Fold Cross-Validation" "ML,regression,validation"
"152" "nnet" "CRAN" "neural networks" "neural_nets,ML"
"153" "gnn" "CRAN" "neural networks" "neural_nets,ML"
"154" "rnn" "CRAN" "neural networks" "neural_nets,ML"
"155" "spnn" "CRAN" "neural networks" "neural_nets,ML"
"156" "brnn" "CRAN" "neural networks" "neural_nets,ML"
"157" "RSNNS" "CRAN" "neural networks" "neural_nets,ML"
"158" "AMORE" "CRAN" "neural networks" "neural_nets,ML"
"159" "simpleNeural" "CRAN" "neural networks" "neural_nets,ML"
"160" "ANN2" "CRAN" "neural networks" "neural_nets,ML"
"161" "yap" "CRAN" "neural networks" "neural_nets,ML"
"162" "yager" "CRAN" "neural networks" "neural_nets,ML"
"163" "deep" "CRAN" "neural networks" "neural_nets,ML"
"164" "neuralnet" "CRAN" "neural networks" "neural_nets,ML"
"165" "nnfor" "CRAN" "neural networks" "neural_nets,ML"
"166" "TeachNet" "CRAN" "neural networks" "neural_nets,ML"
"167" "deepnet" "CRAN" "deep learning" "neural_nets,ML"
"168" "RcppDL" "CRAN" "deep learning" "neural_nets,ML"
"169" "tensorflow" "CRAN" "deep learning" "neural_nets,ML"
"170" "h2o" "CRAN" "deep learning" "neural_nets,ML"
"171" "kerasR" "CRAN" "deep learning" "neural_nets,ML"
"172" "deepNN" "CRAN" "deep learning" "neural_nets,ML"
"173" "Buddle" "CRAN" "deep learning" "neural_nets,ML"
"174" "automl" "CRAN" "deep learning" "neural_nets,ML"
"175" "RLT" "CRAN" "reinforcement learning" "reinforcement_learning,ML"
"176" "ReinforcementLearning" "CRAN" "reinforcement learning" "reinforcement_learning,ML"
"177" "MDPtoolbox" "CRAN" "reinforcement learning" "reinforcement_learning,ML"
"178" "Local" "CRAN" "Interpretable Model-Agnostic Explanations (lime) CRAN explaining the outcome of black box models" "model_explanation,ML"
"179" "localModel" "CRAN" "LIME-Based Explanations with Interpretable Inputs Based on Ceteris Paribus Profiles" "model_explanation,ML"
"180" "iml" "CRAN" "Interpretable Machine Learning " "model_explanation,ML"
"181" "EIX" "CRAN" "Explain Interactions in XGBoost" "model_explanation,ML"
"182" "flashlight" "CRAN" "Shed light on black box machine learning models by the help of model performance, variable importance, global surrogate models, ICE profiles, partial dependencw" "model_explanation,ML"
"183" "interpret" "CRAN" "Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and interpretable characteristics" "model_explanation,ML"
"184" "outliertree" "CRAN" "Outlier detection method that flags suspicious values within observations, constrasting them against the normal values in a user-readable format" "model_explanation,ML"
"185" "breakDown" "CRAN" "The breakDown package is a model agnostic tool for decomposition of predictions from black boxes. Break Down Table shows contributions of every variable to a final prediction. Break Down Plot presents variable contributions in a concise graphical way. This package works for binary classifiers and general regression models. model_explanation,ML" "model_explanation,ML"
"186" "NMF" "CRAN" "Provides a bunch of functions, including one for regularised NMF" "matrix_factorisation,data_analysis"
"187" "FABIA" "?" "Factor Analysis for Bicluster Acquisition CRAN Biclustering by Factor Analysis for Bicluster Acquisition (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously matrix_factorisation,data_analysis" "matrix_factorisation,data_analysis"
"188" "rNMF" "?" "robust NMF" "matrix_factorisation,data_analysis"
"189" "Non-negative" "?" "Factorization-based Immune-TUmor MIcroenvironment Deconvolution (NITUMID) CRAN Current version of NITUMID only supports tumor microenvironment deconvolution for bulk melanoma data matrix_factorisation,bioinformatics,data_analysis" "matrix_factorisation,data_analysis"
"190" "rsparse" "?" "Fast and accurate machine learning on sparse matrices - matrix factorizations, regression, classification, top-N recommendations" "matrix_factorisation,regression,data_analysis"
"191" "diceR" "?" NA "matrix_factorisation,data_analysis"
"192" "SWNE" "?" "Weighted Nonnegative Embedding (SWNE) CRAN Adaptation of Onco-GPS with mapping to low dimensions using Salmon mapping" "matrix_factorisation,bioinformatics,plot,data_analysis"
"193" "fastICA" "?" "ICA" "matrix_factorisation,data_analysis"
"194" "matrix_factorisation,bioinformatics,data_integration,data_analysis" "?" "matrix_factorisation,bioinformatics,data_integration,data_analysis" "matrix_factorisation,data_analysis"
"195" "MOFAtools" "?" "MOFA is a factor analysis model that provides a general framework for the integration of multi-omic data sets in a completely unsupervised fashion" "matrix_factorisation,bioinformatics,data_integration,data_analysis"
"196" "ccfindR" "?" "single-cell RNA-seq analysis using Bayesian non-negative matrix factorization" "matrix_factorisation,bioinformatics,data_analysis"
"197" "scCOGAPS" "?" "matrix factorisation, data integration" "matrix_factorisation,bioinformatics,data_integration,data_analysis"
"198" "LIGER" "?" "Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity " "matrix_factorisation,bioinformatics,data_integration,data_analysis"
"199" "irlba" "CRAN" "Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices" "matrix_factorisation,data_analysis"