R-universe search: manipulate

tidyverse

dplyr:A Grammar of Data Manipulation

A fast, consistent tool for working with data frame like objects, both in memory and out of memory.

Maintained by Hadley Wickham. Last updated 13 days ago.

data-manipulation grammar cpp

12.8 match 4.8k stars 24.68 score 659k scripts 7.8k dependents

jjallaire

manipulate:Interactive Plots for RStudio

Interactive plotting functions for use within RStudio. The manipulate function accepts a plotting expression and a set of controls (e.g. slider, picker, checkbox, or button) which are used to dynamically change values within the expression. When a value is changed using its corresponding control the expression is automatically re-executed and the plot is redrawn.

Maintained by JJ Allaire. Last updated 10 years ago.

59.1 match 1 stars 5.29 score 812 scripts 18 dependents

colearendt

xlsx:Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files

Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.

Maintained by Cole Arendt. Last updated 3 years ago.

excel java rjava xlsx openjdk

17.1 match 85 stars 14.40 score 14k scripts 35 dependents

thomasp85

tidygraph:A Tidy API for Graph Manipulation

A graph, while not "tidy" in itself, can be thought of as two tidy data frames describing node and edge data respectively. 'tidygraph' provides an approach to manipulate these two virtual data frames using the API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms.

Maintained by Thomas Lin Pedersen. Last updated 1 months ago.

graph-algorithms graph-manipulation igraph network-analysis tidyverse cpp

14.8 match 553 stars 14.74 score 4.6k scripts 136 dependents

cynkra

dm:Relational Data Models

Provides tools for working with multiple related tables, stored as data frames or in a relational database. Multiple tables (data and metadata) are stored in a compound object, which can then be manipulated with a pipe-friendly syntax.

Maintained by Kirill Müller. Last updated 2 months ago.

data-model data-warehousing datawarehousing dbi dbplyr relational-databases

14.4 match 511 stars 14.81 score 410 scripts 8 dependents

sebkrantz

collapse:Advanced and Fast Data Transformation

A C/C++ based package for advanced data transformation and statistical computing in R that is extremely fast, class-agnostic, robust and programmer friendly. Core functionality includes a rich set of S3 generic grouped and weighted statistical functions for vectors, matrices and data frames, which provide efficient low-level vectorizations, OpenMP multithreading, and skip missing values by default. These are integrated with fast grouping and ordering algorithms (also callable from C), and efficient data manipulation functions. The package also provides a flexible and rigorous approach to time series and panel data in R. It further includes fast functions for common statistical procedures, detailed (grouped, weighted) summary statistics, powerful tools to work with nested data, fast data object conversions, functions for memory efficient R programming, and helpers to effectively deal with variable labels, attributes, and missing data. It is well integrated with base R classes, 'dplyr'/'tibble', 'data.table', 'sf', 'units', 'plm' (panel-series and data frames), and 'xts'/'zoo'.

Maintained by Sebastian Krantz. Last updated 6 days ago.

data-aggregation data-analysis data-manipulation data-processing data-science data-transformation econometrics high-performance panel-data scientific-computing statistics time-series weighted weights cpp openmp

11.3 match 672 stars 16.63 score 708 scripts 97 dependents

jonclayden

shades:Simple Colour Manipulation

Functions for easily manipulating colours, creating colour scales and calculating colour distances.

Maintained by Jon Clayden. Last updated 5 months ago.

color color-manipulation colour colour-manipulation colour-spaces

18.9 match 83 stars 9.58 score 178 scripts 37 dependents

tidyverse

stringr:Simple, Consistent Wrappers for Common String Operations

A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.

Maintained by Hadley Wickham. Last updated 7 months ago.

regular-expression strings

7.0 match 622 stars 21.97 score 164k scripts 8.2k dependents

easystats

datawizard:Easy Data Wrangling and Statistical Transformations

A lightweight package to assist in key steps involved in any data analysis workflow: (1) wrangling the raw data to get it in the needed form, (2) applying preprocessing steps and statistical transformations, and (3) compute statistical summaries of data properties and distributions. It is also the data wrangling backend for packages in 'easystats' ecosystem. References: Patil et al. (2022) <doi:10.21105/joss.04684>.

Maintained by Etienne Bacher. Last updated 10 days ago.

data dplyr hacktoberfest janitor manipulation reshape tidyr wrangling

10.0 match 222 stars 14.71 score 436 scripts 119 dependents

r-spatial

sf:Simple Features for R

Support for simple feature access, a standardized way to encode and analyze spatial vector data. Binds to 'GDAL' <doi: 10.5281/zenodo.5884351> for reading and writing data, to 'GEOS' <doi: 10.5281/zenodo.11396894> for geometrical operations, and to 'PROJ' <doi: 10.5281/zenodo.5884394> for projection conversions and datum transformations. Uses by default the 's2' package for geometry operations on geodetic (long/lat degree) coordinates.

Maintained by Edzer Pebesma. Last updated 16 days ago.

gdal geos proj spatial cpp

6.5 match 1.4k stars 22.42 score 117k scripts 1.2k dependents

aphalo

gginnards:Explore the Innards of 'ggplot2' Objects

Extensions to 'ggplot2' providing low-level debug tools: statistics and geometries echoing their data argument. Layer manipulation: deletion, insertion, extraction and reordering of layers. Deletion of unused variables from the data object embedded in "ggplot" objects.

Maintained by Pedro J. Aphalo. Last updated 3 months ago.

dataviz debugging ggplot2-enhancementes ggplot2-layer-manipulation inspection

15.6 match 25 stars 9.03 score 378 scripts 3 dependents

brodieg

fansi:ANSI Control Sequence Aware String Functions

Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.

Maintained by Brodie Gaslam. Last updated 10 months ago.

string-manipulation

9.8 match 54 stars 14.18 score 136 scripts 11k dependents

ropensci

magick:Advanced Graphics and Image-Processing in R

Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.

Maintained by Jeroen Ooms. Last updated 20 days ago.

image-manipulation image-processing imagemagick cpp

8.0 match 468 stars 17.31 score 9.0k scripts 256 dependents

gagolews

stringi:Fast and Portable Character String Processing Facilities

A collection of character string/text/natural language processing tools for pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date-time formatting and parsing, and many more. They are fast, consistent, convenient, and - thanks to 'ICU' (International Components for Unicode) - portable across all locales and platforms. Documentation about 'stringi' is provided via its website at <https://stringi.gagolewski.com/> and the paper by Gagolewski (2022, <doi:10.18637/jss.v103.i02>).

Maintained by Marek Gagolewski. Last updated 1 months ago.

icu icu4c natural-language-processing nlp regex regexp string-manipulation stringi stringr text text-processing tidy-data unicode cpp

7.5 match 309 stars 18.31 score 10k scripts 8.6k dependents

emilhvitfeldt

prismatic:Color Manipulation Tools

Manipulate and visualize colors in a intuitive, low-dependency and functional way.

Maintained by Emil Hvitfeldt. Last updated 4 months ago.

color color-manipulation colour

11.4 match 138 stars 11.65 score 428 scripts 29 dependents

bioc

universalmotif:Import, Modify, and Export Motifs with R

Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.

Maintained by Benjamin Jean-Marie Tremblay. Last updated 4 months ago.

motifannotation motifdiscovery dataimport generegulation motif-analysis motif-enrichment-analysis sequence-logo cpp

10.1 match 28 stars 11.04 score 342 scripts 12 dependents

bioc

GenomicRanges:Representation and manipulation of genomic intervals

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.

Maintained by Hervé Pagès. Last updated 4 months ago.

genetics infrastructure datarepresentation sequencing annotation genomeannotation coverage bioconductor-package core-package

6.0 match 44 stars 17.75 score 13k scripts 1.3k dependents

rstudio

rstudioapi:Safely Access the RStudio API

Access the RStudio API (if available) and provide informative error messages when it's not.

Maintained by Kevin Ushey. Last updated 4 months ago.

5.5 match 172 stars 18.81 score 3.6k scripts 2.1k dependents

r-forge

colorspace:A Toolbox for Manipulating and Assessing Colors and Palettes

Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/> and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, <doi:10.18637/jss.v096.i01>).

Maintained by Achim Zeileis. Last updated 4 months ago.

6.4 match 16.23 score 8.2k scripts 8.1k dependents

geobosh

Rdpack:Update and Manipulate Rd Documentation Objects

Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.

Maintained by Georgi N. Boshnakov. Last updated 13 hours ago.

bibtex bibtex-references citations documentation rd-format roxygen2

7.5 match 30 stars 13.76 score 73 scripts 2.3k dependents

bioc

AnnotationDbi:Manipulation of SQLite-based annotations in Bioconductor

Implements a user-friendly interface for querying SQLite-based annotation data packages.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

annotation microarray sequencing genomeannotation bioconductor-package core-package

6.5 match 9 stars 15.05 score 3.6k scripts 769 dependents

fastverse

fastverse:A Suite of High-Performance Packages for Statistics and Data Manipulation

Easy installation, loading and management, of high-performance packages for statistical computing and data manipulation in R. The core 'fastverse' consists of 4 packages: 'data.table', 'collapse', 'kit' and 'magrittr', that jointly only depend on 'Rcpp'. The 'fastverse' can be freely and permanently extended with additional packages, both globally or for individual projects. Separate package verses can also be created. Fast packages for many common tasks such as time series, dates and times, strings, spatial data, statistics, data serialization, larger-than-memory processing, and compilation of R code are listed in the README file: <https://github.com/fastverse/fastverse#suggested-extensions>.

Maintained by Sebastian Krantz. Last updated 25 days ago.

c cpp data-aggregation data-manipulation data-science data-transformation high-performance low-dependency panel-data statistical-computing time-series weights

10.9 match 264 stars 8.90 score 222 scripts

bioc

Rsamtools:Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.

dataimport sequencing coverage alignment qualitycontrol bioconductor-package core-package curl bzip2 xz-utils zlib cpp

6.1 match 28 stars 15.42 score 3.2k scripts 566 dependents

rte-antares-rpackage

manipulateWidget:Add Even More Interactivity to Interactive Charts

Like package 'manipulate' does for static graphics, this package helps to easily add controls like sliders, pickers, checkboxes, etc. that can be used to modify the input data or the parameters of an interactive chart created with package 'htmlwidgets'.

Maintained by Veronique Bachelier. Last updated 3 years ago.

graphical htmlwidgets interactive-charts manipulate rte shiny tyndp

10.5 match 129 stars 8.82 score 143 scripts 1 dependents

trinker

textshape:Tools for Reshaping Text

Tools that can be used to reshape and restructure text data.

Maintained by Tyler Rinker. Last updated 12 months ago.

data-reshaping manipulation sentence-boundary-detection text-data text-formating tidy

10.0 match 50 stars 9.18 score 266 scripts 34 dependents

r-lidar

lidR:Airborne LiDAR Data Manipulation and Visualization for Forestry Applications

Airborne LiDAR (Light Detection and Ranging) interface for data manipulation and visualization. Read/write 'las' and 'laz' files, computation of metrics in area based approach, point filtering, artificial point reduction, classification from geographic data, normalization, individual tree segmentation and other manipulations.

Maintained by Jean-Romain Roussel. Last updated 1 months ago.

als forestry las laz lidar point-cloud remote-sensing openblas cpp openmp

6.0 match 623 stars 14.47 score 844 scripts 8 dependents

yulab-smu

tidytree:A Tidy Tool for Phylogenetic Tree Data Manipulation

Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.

Maintained by Guangchuang Yu. Last updated 8 months ago.

phylogenetic-tree tidyverse tree-data

6.3 match 54 stars 13.25 score 584 scripts 128 dependents

davidgohel

officer:Manipulation of Microsoft Word and PowerPoint Documents

Access and manipulate 'Microsoft Word', 'RTF' and 'Microsoft PowerPoint' documents from R. The package focuses on tabular and graphical reporting from R; it also provides two functions that let users get document content into data objects. A set of functions lets add and remove images, tables and paragraphs of text in new or existing documents. The package does not require any installation of Microsoft products to be able to write Microsoft files.

Maintained by David Gohel. Last updated 1 months ago.

ms-office-documents powerpoint word

5.3 match 630 stars 15.79 score 4.1k scripts 137 dependents

nathaneastwood

poorman:A Poor Man's Dependency Free Recreation of 'dplyr'

A replication of key functionality from 'dplyr' and the wider 'tidyverse' using only 'base'.

Maintained by Nathan Eastwood. Last updated 1 years ago.

base-r data-manipulation grammar

7.5 match 341 stars 10.79 score 156 scripts 27 dependents

bioc

IRanges:Foundation of integer range manipulation in Bioconductor

Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.

Maintained by Hervé Pagès. Last updated 1 months ago.

infrastructure datarepresentation bioconductor-package core-package

5.3 match 22 stars 15.09 score 2.1k scripts 1.8k dependents

kkholst

mets:Analysis of Multivariate Event Times

Implementation of various statistical models for multivariate event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>. Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray, Ghosh-Lin, Binomial regression) with fast computation of influence functions.

Maintained by Klaus K. Holst. Last updated 3 days ago.

multivariate-time-to-event survival-analysis time-to-event fortran openblas cpp

5.9 match 14 stars 13.47 score 236 scripts 42 dependents

ropensci

frictionless:Read and Write Frictionless Data Packages

Read and write Frictionless Data Packages. A 'Data Package' (<https://specs.frictionlessdata.io/data-package/>) is a simple container format and standard to describe and package a collection of (tabular) data. It is typically used to publish FAIR (<https://www.go-fair.org/fair-principles/>) and open datasets.

Maintained by Peter Desmet. Last updated 6 months ago.

frictionlessdata oscibio

8.0 match 30 stars 9.79 score 55 scripts 6 dependents

igraph

igraph:Network Analysis and Visualization

Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.

Maintained by Kirill Müller. Last updated 15 hours ago.

complex-networks graph-algorithms graph-theory mathematics network-analysis network-graph fortran libxml2 glpk openblas cpp

3.6 match 582 stars 21.11 score 31k scripts 1.9k dependents

r-gregmisc

gdata:Various R Programming Tools for Data Manipulation

Various R programming tools for data manipulation, including medical unit conversions, combining objects, character vector operations, factor manipulation, obtaining information about R objects, generating fixed-width format files, extracting components of date & time objects, operations on columns of data frames, matrix operations, operations on vectors, operations on data frames, value of last evaluated expression, and a resample() wrapper for sample() that ensures consistent behavior for both scalar and vector arguments.

Maintained by Arni Magnusson. Last updated 2 months ago.

5.4 match 9 stars 13.62 score 4.5k scripts 124 dependents

crunch-io

crunch:Crunch.io Data Tools

The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.

Maintained by Greg Freedman Ellis. Last updated 11 days ago.

7.0 match 9 stars 10.53 score 200 scripts 2 dependents

emmanuelparadis

ape:Analyses of Phylogenetics and Evolution

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Maintained by Emmanuel Paradis. Last updated 16 hours ago.

openblas cpp

4.3 match 64 stars 17.22 score 13k scripts 599 dependents

bioc

ShortRead:FASTQ input and manipulation

This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

dataimport sequencing qualitycontrol bioconductor-package core-package zlib cpp

5.8 match 8 stars 12.08 score 1.8k scripts 49 dependents

hope-data-science

tidyfst:Tidy Verbs for Fast Data Manipulation

A toolkit of tidy data manipulation verbs with 'data.table' as the backend. Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table', 'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain. This package is an extension of 'data.table'. While enjoying a tidy syntax, it also wraps combinations of efficient functions to facilitate frequently-used data operations.

Maintained by Tian-Yuan Huang. Last updated 6 months ago.

7.0 match 98 stars 10.09 score 118 scripts 4 dependents

bouldercodehub

RWDataPlyr:Read and Manipulate Data from 'RiverWare'

A tool to read and manipulate data generated from 'RiverWare'(TM) <http://www.riverware.org/> simulations. 'RiverWare' and 'RiverSMART' generate data in "rdf", "csv", and "nc" format. This package provides an interface to read, aggregate, and summarize data from one or more simulations in a 'dplyr' pipeline.

Maintained by Alan Butler. Last updated 2 years ago.

data-manipulation riverware cpp

12.4 match 4 stars 5.66 score 77 scripts

bioc

plyranges:A fluent interface for manipulating GenomicRanges

A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased.

Maintained by Michael Love. Last updated 5 months ago.

infrastructure datarepresentation workflowstep coverage bioconductor data-analysis dplyr genomic-ranges genomics tidy-data

5.4 match 143 stars 12.60 score 1.9k scripts 20 dependents

vspinu

timechange:Efficient Manipulation of Date-Times

Efficient routines for manipulation of date-time objects while accounting for time-zones and daylight saving times. The package includes utilities for updating of date-time components (year, month, day etc.), modification of time-zones, rounding of date-times, period addition and subtraction etc. Parts of the 'CCTZ' source code, released under the Apache 2.0 License, are included in this package. See <https://github.com/google/cctz> for more details.

Maintained by Vitalie Spinu. Last updated 1 years ago.

ceiling date-time period rounding time time-zones update cpp

5.6 match 31 stars 12.11 score 68 scripts 1.9k dependents

ropensci

ijtiff:Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files

General purpose TIFF file I/O for R users. Currently the only such package with read and write support for TIFF files with floating point (real-numbered) pixels, and the only package that can correctly import TIFF files that were saved from 'ImageJ' and write TIFF files than can be correctly read by 'ImageJ' <https://imagej.net/ij/>. Also supports text image I/O.

Maintained by Rory Nolan. Last updated 6 days ago.

image-manipulation imagej peer-reviewed tiff-files tiff-images tiff

7.5 match 18 stars 8.97 score 36 scripts 7 dependents

sticsrpacks

SticsRFiles:Read and Modify 'STICS' Input/Output Files

Manipulating input and output files of the 'STICS' crop model. Files are either 'JavaSTICS' XML files or text files used by the model 'fortran' executable. Most basic functionalities are reading or writing parameter names and values in both XML or text input files, and getting data from output files. Advanced functionalities include XML files generation from XML templates and/or spreadsheets, or text files generation from XML files by using 'xslt' transformation.

Maintained by Patrice Lecharpentier. Last updated 18 days ago.

8.0 match 4 stars 8.27 score 124 scripts

thibautjombart

adegenet:Exploratory Analysis of Genetic and Genomic Data

Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

Maintained by Zhian N. Kamvar. Last updated 1 months ago.

5.2 match 182 stars 12.60 score 1.9k scripts 29 dependents

bioc

Biostrings:Efficient manipulation of biological strings

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Maintained by Hervé Pagès. Last updated 24 days ago.

sequencematching alignment sequencing genetics dataimport datarepresentation infrastructure bioconductor-package core-package

3.7 match 61 stars 17.83 score 8.6k scripts 1.2k dependents

cran

bnlearn:Bayesian Network Structure Learning, Parameter Learning and Inference

Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries, cross-validation, bootstrap and model averaging. Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.

Maintained by Marco Scutari. Last updated 2 months ago.

openblas

8.3 match 57 stars 7.72 score 32 dependents

r-lib

desc:Manipulate DESCRIPTION Files

Tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.

Maintained by Gábor Csárdi. Last updated 1 months ago.

4.2 match 123 stars 14.68 score 409 scripts 1.1k dependents

yihui

xfun:Supporting Functions for Packages Maintained by 'Yihui Xie'

Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.

Maintained by Yihui Xie. Last updated 3 days ago.

3.3 match 145 stars 18.18 score 916 scripts 4.4k dependents

r-dbi

DBI:R Database Interface

A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

Maintained by Kirill Müller. Last updated 3 months ago.

database interface

2.9 match 302 stars 20.88 score 19k scripts 2.9k dependents

insightsengineering

rtables:Reporting Tables

Reporting tables often have structure that goes beyond simple rectangular data. The 'rtables' package provides a framework for declaring complex multi-level tabulations and then applying them to data. This framework models both tabulation and the resulting tables as hierarchical, tree-like objects which support sibling sub-tables, arbitrary splitting or grouping of data in row and column dimensions, cells containing multiple values, and the concept of contextual summary computations. A convenient pipe-able interface is provided for declaring table layouts and the corresponding computations, and then applying them to data.

Maintained by Joe Zhu. Last updated 2 months ago.

pharmaceuticals tables

4.3 match 232 stars 13.65 score 238 scripts 17 dependents

eblondel

geosapi:GeoServer REST API R Interface

Provides an R interface to the GeoServer REST API, allowing to upload and publish data in a GeoServer web-application and expose data to OGC Web-Services. The package currently supports all CRUD (Create,Read,Update,Delete) operations on GeoServer workspaces, namespaces, datastores (stores of vector data), featuretypes, layers, styles, as well as vector data upload operations. For more information about the GeoServer REST API, see <https://docs.geoserver.org/stable/en/user/rest/>.

Maintained by Emmanuel Blondel. Last updated 15 days ago.

api geoserver gis publication rest spatial

9.4 match 34 stars 6.23 score 33 scripts

rorynolan

strex:Extra String Manipulation Functions

There are some things that I wish were easier with the 'stringr' or 'stringi' packages. The foremost of these is the extraction of numbers from strings. 'stringr' and 'stringi' make you figure out the regular expression for yourself; 'strex' takes care of this for you. There are many other handy functionalities in 'strex'. Contributions to this package are encouraged; it is intended as a miscellany of string manipulation functions that cannot be found in 'stringi' or 'stringr'.

Maintained by Rory Nolan. Last updated 6 months ago.

5.4 match 41 stars 10.59 score 1.2k scripts 18 dependents

schochastics

graphlayouts:Additional Layout Algorithms for Network Visualizations

Several new layout algorithms to visualize networks are provided which are not part of 'igraph'. Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow the user to emphasize hidden group structures in networks or focus on specific nodes.

Maintained by David Schoch. Last updated 2 months ago.

ggraph graph-algorithms network-analysis network-visualization cpp

4.5 match 276 stars 12.52 score 322 scripts 111 dependents

enricoschumann

textutils:Utilities for Handling Strings and Text

Utilities for handling character vectors that store human-readable text (either plain or with markup, such as HTML or LaTeX). The package provides, in particular, functions that help with the preparation of plain-text reports, e.g. for expanding and aligning strings that form the lines of such reports. The package also provides generic functions for transforming R objects to HTML and to plain text.

Maintained by Enrico Schumann. Last updated 2 months ago.

html5 string-manipulation

7.5 match 11 stars 7.37 score 47 scripts 12 dependents

r-lib

ps:List, Query, Manipulate System Processes

List, query and manipulate all system processes, on 'Windows', 'Linux' and 'macOS'.

Maintained by Gábor Csárdi. Last updated 17 days ago.

3.6 match 79 stars 15.09 score 108 scripts 1.5k dependents

bioc

CellBench:Construct Benchmarks for Single Cell Analysis Methods

This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods.

Maintained by Shian Su. Last updated 5 months ago.

software infrastructure singlecell benchmark bioinformatics

6.2 match 30 stars 8.71 score 98 scripts

clugen

clugenr:Multidimensional Cluster Generation Using Support Lines

An implementation of the clugen algorithm for generating multidimensional clusters with arbitrary distributions. Each cluster is supported by a line segment, the position, orientation and length of which guide where the respective points are placed. This package is described in Fachada & de Andrade (2023) <doi:10.1016/j.knosys.2023.110836>.

Maintained by Nuno Fachada. Last updated 7 months ago.

multidimensional-clusters multidimensional-data synthetic-clusters synthetic-data-generator synthetic-dataset-generation

10.0 match 5 stars 5.39 score 14 scripts

wahani

dat:Tools for Data Manipulation

An implementation of common higher order functions with syntactic sugar for anonymous function. Provides also a link to 'dplyr' and 'data.table' for common transformations on data frames to work around non standard evaluation by default.

Maintained by Sebastian Warnholz. Last updated 4 years ago.

8.0 match 16 stars 6.66 score 32 scripts 1 dependents

biodiverse

unmarked:Models for Data from Unmarked Animals

Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.

Maintained by Ken Kellner. Last updated 1 days ago.

openblas cpp openmp

4.0 match 4 stars 13.03 score 652 scripts 12 dependents

dynverse

dynutils:Common Functionality for the 'dynverse' Packages

Provides common functionality for the 'dynverse' packages. 'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods. For more information, check out <https://dynverse.org>.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

cpp

7.5 match 3 stars 6.89 score 109 scripts 8 dependents

larmarange

labelled:Manipulating Labelled Data

Work with labelled data imported from 'SPSS' or 'Stata' with 'haven' or 'foreign'. This package provides useful functions to deal with "haven_labelled" and "haven_labelled_spss" classes introduced by 'haven' package.

Maintained by Joseph Larmarange. Last updated 26 days ago.

haven labels metadata sas spss stata

3.3 match 76 stars 15.02 score 2.4k scripts 96 dependents

psolymos

mefa4:Multivariate Data Handling with S4 Classes and Sparse Matrices

An S4 update of the 'mefa' package using sparse matrices for enhanced efficiency. Sparse array-like objects are supported via lists of sparse matrices.

Maintained by Peter Solymos. Last updated 6 months ago.

data-manipulation ecology sparse-matrices

9.3 match 5.34 score 368 scripts 2 dependents

knausb

vcfR:Manipulate and Visualize VCF Data

Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.

Maintained by Brian J. Knaus. Last updated 23 days ago.

genomics population-genetics population-genomics rcpp vcf-data visualization zlib cpp

3.6 match 254 stars 13.59 score 3.1k scripts 19 dependents

rorynolan

filesstrings:Handy File and String Manipulation

This started out as a package for file and string manipulation. Since then, the 'fs' and 'strex' packages emerged, offering functionality previously given by this package (but it's done better in these new ones). Those packages have hence almost pushed 'filesstrings' into extinction. However, it still has a small number of unique, handy file manipulation functions which can be seen in the vignette. One example is a function to remove spaces from all file names in a directory.

Maintained by Rory Nolan. Last updated 1 years ago.

5.7 match 22 stars 8.59 score 632 scripts 4 dependents

yulab-smu

seqmagick:Sequence Manipulation Utilities

Supports reading and writing sequences for different formats (currently interleaved and sequential formats for 'FASTA' and 'PHYLIP'), file conversion, and manipulation (e.g. filter sequences that contain specify pattern, export consensus sequence from an alignment).

Maintained by Guangchuang Yu. Last updated 1 years ago.

8.7 match 6 stars 5.64 score 8 scripts 3 dependents

zilong-li

vcfppR:Rapid Manipulation of the Variant Call Format (VCF)

The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.

Maintained by Zilong Li. Last updated 3 days ago.

bioinformatics fastr htslib population-genetics population-genomics vcf vcf-data visulization libdeflate zlib bzip2 xz-utils curl cpp

7.3 match 13 stars 6.70 score 16 scripts

gergness

srvyr:'dplyr'-Like Syntax for Summary Statistics of Survey Data

Use piping, verbs like 'group_by' and 'summarize', and other 'dplyr' inspired syntactic style when calculating summary statistics on survey data using functions from the 'survey' package.

Maintained by Greg Freedman Ellis. Last updated 1 months ago.

survey

3.5 match 215 stars 13.88 score 1.8k scripts 15 dependents

tidyverse

lubridate:Make Dealing with Dates a Little Easier

Functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and time-span objects. The 'lubridate' package has a consistent and memorable syntax that makes working with dates easy and fun.

Maintained by Vitalie Spinu. Last updated 3 months ago.

date date-time

2.3 match 757 stars 20.95 score 135k scripts 1.9k dependents

renkun-ken

rlist:A Toolbox for Non-Tabular Data Manipulation

Provides a set of functions for data manipulation with list objects, including mapping, filtering, grouping, sorting, updating, searching, and other useful functions. Most functions are designed to be pipeline friendly so that data processing with lists can be chained.

Maintained by Kun Ren. Last updated 2 years ago.

3.5 match 206 stars 13.73 score 2.2k scripts 123 dependents

bioc

GenomicAlignments:Representation and manipulation of short genomic alignments

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Maintained by Hervé Pagès. Last updated 5 months ago.

infrastructure dataimport genetics sequencing rnaseq snp coverage alignment immunooncology bioconductor-package core-package

3.5 match 10 stars 13.61 score 3.1k scripts 529 dependents

krzjoa

matricks:Useful Tricks for Matrix Manipulation

Provides functions, which make matrix creation conciser (such as the core package's function m() for rowwise matrix definition or runifm() for random value matrices). Allows to set multiple matrix values at once, by using list of formulae. Provides additional matrix operators and dedicated plotting function.

Maintained by Krzysztof Joachimiak. Last updated 5 years ago.

algebra matrix matrix-manipulation cpp

10.6 match 4 stars 4.51 score 16 scripts

mandymejia

ciftiTools:Tools for Reading, Writing, Viewing and Manipulating CIFTI Files

CIFTI files contain brain imaging data in "grayordinates," which represent the gray matter as cortical surface vertices (left and right) and subcortical voxels (cerebellum, basal ganglia, and other deep gray matter). 'ciftiTools' provides a unified environment for reading, writing, visualizing and manipulating CIFTI-format data. It supports the "dscalar," "dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti" object, which is structured for convenient access to the data and metadata, and includes support for surface geometry files to enable spatially-dependent functionality such as static or interactive visualizations and smoothing.

Maintained by Amanda Mejia. Last updated 2 months ago.

5.4 match 47 stars 8.90 score 176 scripts 4 dependents

rte-antares-rpackage

antaresRead:Import, Manipulate and Explore the Results of an 'Antares' Simulation

Import, manipulate and explore results generated by 'Antares', a powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems (more information about 'Antares' here : <https://antares-simulator.org/>).

Maintained by Tatiana Vargas. Last updated 3 days ago.

infrastructure dataimport adequacy bilan electricity energy hdf5 linear-algebra monte-carlo-simulation optimisation previsionnel rhdf5 rte simulation tyndp

4.9 match 13 stars 9.45 score 148 scripts 3 dependents

ropensci

treedata.table:Manipulation of Matched Phylogenies and Data using 'data.table'

An implementation that combines trait data and a phylogenetic tree (or trees) into a single object of class treedata.table. The resulting object can be easily manipulated to simultaneously change the trait- and tree-level sampling. Currently implemented functions allow users to use a 'data.table' syntax when performing operations on the trait dataset within the treedata.table object.

Maintained by Cristian Roman-Palacios. Last updated 4 years ago.

9.0 match 7 stars 5.12 score 25 scripts

ropensci

rdflib:Tools to Manipulate and Query Semantic Data

The Resource Description Framework, or 'RDF' is a widely used data representation model that forms the cornerstone of the Semantic Web. 'RDF' represents data as a graph rather than the familiar data table or rectangle of relational databases. The 'rdflib' package provides a friendly and concise user interface for performing common tasks on 'RDF' data, such as reading, writing and converting between the various serializations of 'RDF' data, including 'rdfxml', 'turtle', 'nquads', 'ntriples', and 'json-ld'; creating new 'RDF' graphs, and performing graph queries using 'SPARQL'. This package wraps the low level 'redland' R package which provides direct bindings to the 'redland' C library. Additionally, the package supports the newer and more developer friendly 'JSON-LD' format through the 'jsonld' package. The package interface takes inspiration from the Python 'rdflib' library.

Maintained by Carl Boettiger. Last updated 7 months ago.

peer-reviewed

4.8 match 57 stars 9.59 score 123 scripts 7 dependents

r-lib

bit:Classes and Methods for Fast Memory-Efficient Boolean Selections

Provided are classes for boolean and skewed boolean vectors, fast boolean methods, fast unique and non-unique integer sorting, fast set operations on sorted and unsorted sets of integers, and foundations for ff (range index, compression, chunked processing).

Maintained by Michael Chirico. Last updated 6 days ago.

3.0 match 12 stars 15.15 score 131 scripts 3.2k dependents

nspyrison

spinifex:Manual Tours, Manual Control of Dynamic Projections of Numeric Multivariate Data

Data visualization tours animates linear projection of multivariate data as its basis (ie. orientation) changes. The 'spinifex' packages generates paths for manual tours by manipulating the contribution of a single variable at a time Cook & Buja (1997) <doi:10.1080/10618600.1997.10474754>. Other types of tours, such as grand (random walk) and guided (optimizing some objective function) are available in the 'tourr' package Wickham et al. <doi:10.18637/jss.v040.i02>. 'spinifex' builds on 'tourr' and can render tours with 'gganimate' and 'plotly' graphics, and allows for exporting as an .html widget and as an .gif, respectively. This work is fully discussed in Spyrison & Cook (2020) <doi:10.32614/RJ-2020-027>.

Maintained by Nicholas Spyrison. Last updated 2 months ago.

dimension reduction tours visualization

7.2 match 3 stars 6.28 score 105 scripts 1 dependents

bioc

GenomeInfoDb:Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

Maintained by Hervé Pagès. Last updated 2 months ago.

genetics datarepresentation annotation genomeannotation bioconductor-package core-package

2.8 match 32 stars 16.46 score 1.3k scripts 1.7k dependents

r-lib

scales:Scale Functions for Visualization

Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.

Maintained by Thomas Lin Pedersen. Last updated 5 months ago.

ggplot2

2.3 match 419 stars 19.88 score 88k scripts 7.9k dependents

winvector

rquery:Relational Query Generator for Data Manipulation at Scale

A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible table modeling step, plus explicit query reasoning and checking.

Maintained by John Mount. Last updated 2 years ago.

4.7 match 110 stars 9.53 score 126 scripts 3 dependents

lrberge

fixest:Fast Fixed-Effects Estimations

Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial. The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://github.com/lrberge/fixest/blob/master/_DOCS/FENmlm_paper.pdf>. Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.

Maintained by Laurent Berge. Last updated 7 months ago.

cpp openmp

3.0 match 387 stars 14.69 score 3.8k scripts 25 dependents

bioc

Spectra:Spectra Infrastructure for Mass Spectrometry Data

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

Maintained by RforMassSpectrometry Package Maintainer. Last updated 10 days ago.

infrastructure proteomics massspectrometry metabolomics bioconductor hacktoberfest mass-spectrometry

3.4 match 41 stars 13.01 score 254 scripts 35 dependents

decisionpatterns

formula.tools:Programmatic Utilities for Manipulating Formulas, Expressions, Calls, Assignments and Other R Objects

These utilities facilitate the programmatic manipulations of formulas, expressions, calls, assignments and other R language objects. These objects all share the same structure: a left-hand side, operator and right-hand side. This packages provides methods for accessing and modifying this structures as well as extracting and replacing names and symbols from these objects.

Maintained by Christopher Brown. Last updated 7 years ago.

4.9 match 17 stars 8.89 score 236 scripts 79 dependents

metrumresearchgroup

mrgsolve:Simulate from ODE-Based Models

Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

Maintained by Kyle T Baron. Last updated 1 months ago.

mrgsolve ode openblas cpp

4.0 match 138 stars 10.90 score 1.2k scripts 3 dependents

pierreroudier

spectacles:Storing, Manipulating and Analysis Spectroscopy and Associated Data

Stores and eases the manipulation of spectra and associated data, with dedicated classes for spatial and soil-related data.

Maintained by Pierre Roudier. Last updated 2 years ago.

7.0 match 11 stars 6.17 score 45 scripts 1 dependents

dreamrs

datamods:Modules to Import and Manipulate Data in 'Shiny'

'Shiny' modules to import data into an application or 'addin' from various sources, and to manipulate them after that.

Maintained by Victor Perrier. Last updated 12 days ago.

shiny shiny-modules

3.6 match 144 stars 12.03 score 174 scripts 7 dependents

thomasp85

farver:High Performance Colour Space Manipulation

The encoding of colour can be handled in many different ways, using different colour spaces. As different colour spaces have different uses, efficient conversion between these representations are important. The 'farver' package provides a set of functions that gives access to very fast colour space conversion and comparisons implemented in C++, and offers speed improvements over the 'convertColor' function in the 'grDevices' package.

Maintained by Thomas Lin Pedersen. Last updated 10 months ago.

color-conversion cpp

3.0 match 136 stars 14.22 score 164 scripts 8.0k dependents

merck

simtrial:Clinical Trial Simulation

Provides some basic routines for simulating a clinical trial. The primary intent is to provide some tools to generate trial simulations for trials with time to event outcomes. Piecewise exponential failure rates and piecewise constant enrollment rates are the underlying mechanism used to simulate a broad range of scenarios such as those presented in Lin et al. (2020) <doi:10.1080/19466315.2019.1697738>. However, the basic generation of data is done using pipes to allow maximum flexibility for users to meet different needs.

Maintained by Yujie Zhao. Last updated 3 days ago.

cpp

4.5 match 21 stars 9.16 score 52 scripts

r-lib

fs:Cross-Platform File System Operations Based on 'libuv'

A cross-platform interface to file system operations, built on top of the 'libuv' C library.

Maintained by Gábor Csárdi. Last updated 4 months ago.

filesystem libuv cpp

2.0 match 370 stars 20.26 score 8.1k scripts 5.2k dependents

melff

memisc:Management of Survey Data and Presentation of Analysis Results

An infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) 'SPSS' and 'Stata' files is provided. Further, the package allows to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to 'LaTeX' and HTML.

Maintained by Martin Elff. Last updated 12 days ago.

survey-data

3.3 match 46 stars 12.34 score 1.2k scripts 13 dependents

leonawicz

tabr:Music Notation Syntax, Manipulation, Analysis and Transcription in R

Provides a music notation syntax and a collection of music programming functions for generating, manipulating, organizing, and analyzing musical information in R. Music syntax can be entered directly in character strings, for example to quickly transcribe short pieces of music. The package contains functions for directly performing various mathematical, logical and organizational operations and musical transformations on special object classes that facilitate working with music data and notation. The same music data can be organized in tidy data frames for a familiar and powerful approach to the analysis of large amounts of structured music data. Functions are available for mapping seamlessly between these formats and their representations of musical information. The package also provides an API to 'LilyPond' (<https://lilypond.org/>) for transcribing musical representations in R into tablature ("tabs") and sheet music. 'LilyPond' is open source music engraving software for generating high quality sheet music based on markup syntax. The package generates 'LilyPond' files from R code and can pass them to the 'LilyPond' command line interface to be rendered into sheet music PDF files or inserted into R markdown documents. The package offers nominal MIDI file output support in conjunction with rendering sheet music. The package can read MIDI files and attempts to structure the MIDI data to integrate as best as possible with the data structures and functionality found throughout the package.

Maintained by Matthew Leonawicz. Last updated 6 months ago.

guitar-tablature lilypond lilypond-api music-analysis music-data music-notation music-programming music-syntax music-transcription sheet-music

5.0 match 132 stars 7.87 score 94 scripts

bioc

DECIPHER:Tools for curating, analyzing, and manipulating biological sequences

A toolset for deciphering and managing biological sequences.

Maintained by Erik Wright. Last updated 5 days ago.

clustering genetics sequencing dataimport visualization microarray qualitycontrol qpcr alignment wholegenome microbiome immunooncology geneprediction openmp

4.7 match 8.40 score 1.1k scripts 14 dependents

gbganalyst

forstringr:String Manipulation Package for Those Familiar with 'Microsoft Excel'

The goal of 'forstringr' is to enable complex string manipulation in R especially to those more familiar with LEFT(), RIGHT(), and MID() functions in Microsoft Excel. The package combines the power of 'stringr' with other manipulation packages such as 'dplyr' and 'tidyr'.

Maintained by Ezekiel Ogundepo. Last updated 6 months ago.

glue regex string

6.6 match 10 stars 5.89 score 26 scripts 1 dependents

great-northern-diver

loon:Interactive Statistical Data Visualization

An extendable toolkit for interactive data visualization and exploration.

Maintained by R. Wayne Oldford. Last updated 2 years ago.

data-analysis data-science data-visualization exploratory-analysis exploratory-data-analysis high-dimensional-data interactive-graphics interactive-visualizations loon python statistical-analysis statistical-graphics statistics tcl-extension tk

4.3 match 48 stars 9.00 score 93 scripts 5 dependents

bioc

graph:graph: A package to handle graph data structures

A package that implements some simple graph handling capabilities.

Maintained by Bioconductor Package Maintainer. Last updated 11 days ago.

graphandnetwork

3.3 match 11.78 score 764 scripts 342 dependents

lme4

lme4:Linear Mixed-Effects Models using 'Eigen' and S4

Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".

Maintained by Ben Bolker. Last updated 3 days ago.

cpp

1.9 match 647 stars 20.69 score 35k scripts 1.5k dependents

bioc

EBImage:Image processing and analysis toolbox for R

EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.

Maintained by Andrzej Oleś. Last updated 5 months ago.

visualization bioinformatics image-analysis image-processing cpp

3.0 match 71 stars 12.89 score 1.5k scripts 33 dependents

reconhub

epicontacts:Handling, Visualisation and Analysis of Epidemiological Contacts

A collection of tools for representing epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.

Maintained by Finlay Campbell. Last updated 2 months ago.

outbreak

4.4 match 15 stars 8.86 score 112 scripts 2 dependents

bioc

GOstats:Tools for manipulating GO and microarrays

A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

annotation go multiplecomparison geneexpression microarray pathways genesetenrichment graphandnetwork

5.5 match 6.93 score 528 scripts 12 dependents

dwinter

pafr:Read, Manipulate and Visualize 'Pairwise mApping Format' Data

Provides functions to read, process and visualize pairwise sequence alignments in the 'PAF' format used by 'minimap2' and other whole-genome aligners. 'minimap2' is described by Li H. (2018) <doi:10.1093/bioinformatics/bty191>.

Maintained by David Winter. Last updated 4 years ago.

5.7 match 71 stars 6.73 score 75 scripts

ggrothendieck

sqldf:Manipulate R Data Frames Using SQL

The sqldf() function is typically passed a single argument which is an SQL select statement where the table names are ordinary R data frame names. sqldf() transparently sets up a database, imports the data frames into that database, performs the SQL select or other statement and returns the result using a heuristic to determine which class to assign to each column of the returned data frame. The sqldf() or read.csv.sql() functions can also be used to read filtered files into R even if the original files are larger than R itself can handle. 'RSQLite', 'RH2', 'RMySQL' and 'RPostgreSQL' backends are supported.

Maintained by G. Grothendieck. Last updated 3 years ago.

2.9 match 250 stars 13.04 score 8.1k scripts 52 dependents

cropmodels

meteor:Meteorological Data Manipulation

A set of functions for weather and climate data manipulation, and other helper functions, to support dynamic ecological modeling, particularly crop and crop disease modeling.

Maintained by Robert J. Hijmans. Last updated 2 years ago.

cpp

8.4 match 3 stars 4.53 score 25 scripts 3 dependents

klausvigo

phangorn:Phylogenetic Reconstruction and Analysis

Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).

Maintained by Klaus Schliep. Last updated 1 months ago.

software technology qualitycontrol phylogenetic-analysis phylogenetics openblas cpp

2.3 match 206 stars 16.69 score 2.5k scripts 135 dependents

geoffjentry

twitteR:R Based Twitter Client

Provides an interface to the Twitter web API.

Maintained by Jeff Gentry. Last updated 9 years ago.

3.7 match 254 stars 10.18 score 2.0k scripts 1 dependents

asardaes

table.express:Build 'data.table' Expressions with Data Manipulation Verbs

A specialization of 'dplyr' data manipulation verbs that parse and build expressions which are ultimately evaluated by 'data.table', letting it handle all optimizations. A set of additional verbs is also provided to facilitate some common operations on a subset of the data.

Maintained by Alexis Sarda-Espinosa. Last updated 2 years ago.

6.4 match 65 stars 5.81 score 8 scripts

kmkuesters

pooledpeaks:Genetic Analysis of Pooled Samples

Analyzing genetic data obtained from pooled samples. This package can read in Fragment Analysis output files, process the data, and score peaks, as well as facilitate various analyses, including cluster analysis, calculation of genetic distances and diversity indices, as well as bootstrap resampling for statistical inference. Specifically tailored to handle genetic data efficiently, researchers can explore population structure, genetic differentiation, and genetic relatedness among samples. We updated some functions from Covarrubias-Pazaran et al. (2016) <doi:10.1186/s12863-016-0365-6> to allow for the use of new file formats and referenced the following to write our genetic analysis functions: Long et al. (2022) <doi:10.1038/s41598-022-04776-0>, Jost (2008) <doi:10.1111/j.1365-294x.2008.03887.x>, Nei (1973) <doi:10.1073/pnas.70.12.3321>, Foulley et al. (2006) <doi:10.1016/j.livprodsci.2005.10.021>, Chao et al. (2008) <doi:10.1111/j.1541-0420.2008.01010.x>.

Maintained by Kathleen Kuesters. Last updated 2 days ago.

7.7 match 1 stars 4.85 score 3 scripts

lrberge

hdd:Easy Manipulation of Out of Memory Data Sets

Hard drive data: Class of data allowing the easy importation/manipulation of out of memory data sets. The data sets are located on disk but look like in-memory, the syntax for manipulation is similar to 'data.table'. Operations are performed "chunk-wise" behind the scene. See <https://lrberge.github.io/hdd/> for more information.

Maintained by Laurent Berge. Last updated 2 years ago.

7.6 match 13 stars 4.81 score 7 scripts

daranzolin

hacksaw:Additional Tools for Splitting and Cleaning Data

Move between data frames and lists more efficiently with precision splitting via 'dplyr' verbs. Easily cast variables to different data types. Keep rows with NAs. Shift row values.

Maintained by David Ranzolin. Last updated 4 years ago.

data-manipulation

7.5 match 34 stars 4.84 score 41 scripts

bioc

SparseArray:High-performance sparse data representation and manipulation in R

The SparseArray package provides array-like containers for efficient in-memory representation of multidimensional sparse data in R (arrays and matrices). The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data: the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN.

Maintained by Hervé Pagès. Last updated 24 days ago.

infrastructure datarepresentation bioconductor-package core-package openmp

2.9 match 8 stars 12.68 score 79 scripts 1.2k dependents

caseyyoungflesh

MCMCvis:Tools to Visualize, Manipulate, and Summarize MCMC Output

Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with Stan, NIMBLE, JAGS, and other software.

Maintained by Casey Youngflesh. Last updated 3 months ago.

3.4 match 38 stars 10.52 score 1.8k scripts 5 dependents

rvlenth

emmeans:Estimated Marginal Means, aka Least-Squares Means

Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.

Maintained by Russell V. Lenth. Last updated 3 days ago.

1.9 match 377 stars 19.19 score 13k scripts 187 dependents

geobosh

rbibutils:Read 'Bibtex' Files and Convert Between Bibliography Formats

Read and write 'Bibtex' files. Convert between bibliography formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam <https://sourceforge.net/projects/bibutils/>. Supports all bibliography formats and character encodings implemented in 'bibutils'.

Maintained by Georgi N. Boshnakov. Last updated 4 months ago.

biblatex bibliography bibtex bibutils conversion endnote pubmed ris-format

3.0 match 13 stars 11.97 score 17 scripts 2.3k dependents

gagolews

stringx:Replacements for Base String Functions Powered by 'stringi'

English is the native language for only 5% of the World population. Also, only 17% of us can understand this text. Moreover, the Latin alphabet is the main one for merely 36% of the total. The early computer era, now a very long time ago, was dominated by the US. Due to the proliferation of the internet, smartphones, social media, and other technologies and communication platforms, this is no longer the case. This package replaces base R string functions (such as grep(), tolower(), sprintf(), and strptime()) with ones that fully support the Unicode standards related to natural language and date-time processing. It also fixes some long-standing inconsistencies, and introduces some new, useful features. Thanks to 'ICU' (International Components for Unicode) and 'stringi', they are fast, reliable, and portable across different platforms.

Maintained by Marek Gagolewski. Last updated 2 months ago.

icu icu4c natural-language-processing nlp regex regexp string-manipulation stringi text text-processing unicode

7.5 match 28 stars 4.75 score 1 scripts

tractor

tractor.base:Read, Manipulate and Visualise Magnetic Resonance Images

Functions for working with magnetic resonance images. Reading and writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive visualisation; flexible image manipulation; metadata and sparse image handling.

Maintained by Jon Clayden. Last updated 2 hours ago.

brain-imaging graph-algorithms parcellation tractography

5.2 match 28 stars 6.79 score 35 scripts 1 dependents

rstudio

htmltools:Tools for HTML

Tools for HTML generation and output.

Maintained by Carson Sievert. Last updated 10 months ago.

2.0 match 218 stars 17.61 score 10k scripts 4.5k dependents

r-prof

profile:Read, Manipulate, and Write Profiler Data

Defines a data structure for profiler data, and methods to read and write from the 'Rprof' and 'pprof' file formats.

Maintained by Kirill Müller. Last updated 3 months ago.

4.8 match 12 stars 7.38 score 44 scripts 1 dependents

environmentalinformatics-marburg

satellite:Handling and Manipulating Remote Sensing Data

Herein, we provide a broad variety of functions which are useful for handling, manipulating, and visualizing satellite-based remote sensing data. These operations range from mere data import and layer handling (eg subsetting), over Raster* typical data wrangling (eg crop, extend), to more sophisticated (pre-)processing tasks typically applied to satellite imagery (eg atmospheric and topographic correction). This functionality is complemented by a full access to the satellite layers' metadata at any stage and the documentation of performed actions in a separate log file. Currently available sensors include Landsat 4-5 (TM), 7 (ETM+), and 8 (OLI/TIRS Combined), and additional compatibility is ensured for the Landsat Global Land Survey data set.

Maintained by Florian Detsch. Last updated 1 years ago.

cpp

3.5 match 22 stars 9.88 score 61 scripts 27 dependents

zarquon42b

Rvcg:Manipulations of Triangular Meshes Based on the 'VCGLIB' API

Operations on triangular meshes based on 'VCGLIB'. This package integrates nicely with the R-package 'rgl' to render the meshes processed by 'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is an open source portable C++ templated library for manipulation, processing and displaying with OpenGL of triangle and tetrahedral meshes. The library, composed by more than 100k lines of code, is released under the GPL license, and it is the base of most of the software tools of the Visual Computing Lab of the Italian National Research Council Institute ISTI <https://vcg.isti.cnr.it/>, like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk <https://github.com/cnr-isti-vclab/vcglib> and patched to work with options determined by the configure script as well as to work with the header files included by 'RcppEigen'.

Maintained by Stefan Schlager. Last updated 5 months ago.

cpp openmp

3.4 match 25 stars 10.05 score 195 scripts 29 dependents

tidyverse

duckplyr:A 'DuckDB'-Backed Version of 'dplyr'

A drop-in replacement for 'dplyr', powered by 'DuckDB' for performance. Offers convenient utilities for working with in-memory and larger-than-memory data while retaining full 'dplyr' compatibility.

Maintained by Kirill Müller. Last updated 5 days ago.

analytics dataframe dplyr duckdb performance

3.0 match 309 stars 11.33 score 220 scripts

tidyverse

forcats:Tools for Working with Categorical Variables (Factors)

Helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, 'anonymising', and manually 'recoding').

Maintained by Hadley Wickham. Last updated 1 years ago.

factor tidyverse

1.8 match 555 stars 18.77 score 21k scripts 1.2k dependents

bioc

clusterExperiment:Compare Clusterings for Single-Cell Sequencing

Provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data sets.

Maintained by Elizabeth Purdom. Last updated 5 months ago.

clustering rnaseq sequencing software singlecell cpp

3.5 match 39 stars 9.63 score 192 scripts 1 dependents

rstudio

DT:A Wrapper of the JavaScript Library 'DataTables'

Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.

Maintained by Joe Cheng. Last updated 3 months ago.

datatables htmlwidgets javascript shiny

1.8 match 604 stars 19.15 score 38k scripts 673 dependents

cran

XML:Tools for Parsing and Generating XML Within R and S-Plus

Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".

Maintained by CRAN Team. Last updated 2 months ago.

libxml2

3.8 match 3 stars 8.87 score 1.3k dependents

bioc

XVector:Foundation of external vector representation and manipulation in Bioconductor

Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk).

Maintained by Hervé Pagès. Last updated 2 months ago.

infrastructure datarepresentation bioconductor-package core-package zlib

2.9 match 2 stars 11.36 score 67 scripts 1.7k dependents

xinweima

rddensity:Manipulation Testing Based on Density Discontinuity

Density discontinuity testing (a.k.a. manipulation testing) is commonly employed in regression discontinuity designs and other program evaluation settings to detect perfect self-selection (manipulation) around a cutoff where treatment/policy assignment changes. This package implements manipulation testing procedures using the local polynomial density estimators: rddensity() to construct test statistics and p-values given a prespecified cutoff, rdbwdensity() to perform data-driven bandwidth selection, and rdplotdensity() to construct density plots.

Maintained by Xinwei Ma. Last updated 5 months ago.

11.1 match 2.97 score 206 scripts 1 dependents

billvenables

polynom:A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations

A collection of functions to implement a class for univariate polynomial manipulations.

Maintained by Bill Venables. Last updated 3 years ago.

3.4 match 1 stars 9.50 score 438 scripts 614 dependents

ohdsi

CohortConstructor:Build and Manipulate Study Cohorts Using a Common Data Model

Create and manipulate study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model.

Maintained by Edward Burn. Last updated 4 days ago.

3.4 match 2 stars 9.71 score 207 scripts 2 dependents

ropensci

cffr:Generate Citation File Format ('cff') Metadata for R Packages

The Citation File Format version 1.2.0 <doi:10.5281/zenodo.5171937> is a human and machine readable file format which provides citation metadata for software. This package provides core utilities to generate and validate this metadata.

Maintained by Diego Hernangómez. Last updated 4 days ago.

attribution citation credit citation-files cff metadata citation-file-format ropensci

3.3 match 26 stars 9.74 score 116 scripts 3 dependents

grunwaldlab

metacoder:Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Reads, plots, and manipulates large taxonomic data sets, like those generated from modern high-throughput sequencing, such as metabarcoding (i.e. amplification metagenomics, 16S metagenomics, etc). It provides a tree-based visualization called "heat trees" used to depict statistics for every taxon in a taxonomy using color and size. It also provides various functions to do common tasks in microbiome bioinformatics on data in the 'taxmap' format defined by the 'taxa' package. The 'metacoder' package is described in the publication by Foster et al. (2017) <doi:10.1371/journal.pcbi.1005404>.

Maintained by Zachary Foster. Last updated 1 months ago.

community-diversity hierarchical metabarcoding pcr taxonomy trees cpp

3.4 match 140 stars 9.64 score 328 scripts

friendly

vcdExtra:'vcd' Extensions and Additions

Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data and the 'gnm' package for Generalized Nonlinear Models. In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of 'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer.

Maintained by Michael Friendly. Last updated 5 months ago.

categorical-data-visualization generalized-linear-models mosaic-plots

3.1 match 24 stars 10.34 score 472 scripts 3 dependents

rstudio

leaflet:Create Interactive Web Maps with the JavaScript 'Leaflet' Library

Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny applications and R Markdown documents.

Maintained by Joe Cheng. Last updated 13 days ago.

gis leaflet-map spatial

1.9 match 821 stars 17.20 score 39k scripts 178 dependents

kenhanscombe

ukbtools:Manipulate and Explore UK Biobank Data

A set of tools to create a UK Biobank <http://www.ukbiobank.ac.uk/> dataset from a UKB fileset (.tab, .r, .html), visualize primary demographic data for a sample subset, query ICD diagnoses, retrieve genetic metadata, read and write standard file formats for genetic analyses.

Maintained by Ken Hanscombe. Last updated 2 years ago.

biobank kcl-sgu uk-biobank ukb

4.8 match 101 stars 6.78 score 118 scripts

zajichek

cheese:Tools for Working with Data During Statistical Analysis

Contains tools for working with data during statistical analysis, promoting flexible, intuitive, and reproducible workflows. There are functions designated for specific statistical tasks such building a custom univariate descriptive table, computing pairwise association statistics, etc. These are built on a collection of data manipulation tools designed for general use that are motivated by the functional programming concept.

Maintained by Alex Zajichek. Last updated 2 years ago.

data-manipulation statistical-analysis

8.0 match 4.00 score 2 scripts

2005m

kit:Data Manipulation Functions Implemented in C

Basic functions, implemented in C, for large data manipulation. Fast vectorised ifelse()/nested if()/switch() functions, psum()/pprod() functions equivalent to pmin()/pmax() plus others which are missing from base R. Most of these functions are callable at C level.

Maintained by Morgan Jacob. Last updated 6 months ago.

openmp

3.5 match 58 stars 9.11 score 92 scripts 5 dependents

jeroen

openssl:Toolkit for Encryption, Signatures and Certificates Based on OpenSSL

Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.

Maintained by Jeroen Ooms. Last updated 1 months ago.

openssl

1.8 match 65 stars 18.00 score 632 scripts 5.0k dependents

markvanderloo

settings:Software Option Settings Manager for R

Provides option settings management that goes beyond R's default 'options' function. With this package, users can define their own option settings manager holding option names, default values and (if so desired) ranges or sets of allowed option values that will be automatically checked. Settings can then be retrieved, altered and reset to defaults with ease. For R programmers and package developers it offers cloning and merging functionality which allows for conveniently defining global and local options, possibly in a multilevel options hierarchy. See the package vignette for some examples concerning functions, S4 classes, and reference classes. There are convenience functions to reset par() and options() to their 'factory defaults'.

Maintained by Mark van der Loo. Last updated 9 months ago.

3.3 match 7 stars 9.32 score 1.0k scripts 36 dependents

guokai8

fctutils:Advanced Factor Manipulation Utilities

Provides a collection of utility functions for manipulating and analyzing factor vectors in R. It offers tools for filtering, splitting, combining, and reordering factor levels based on various criteria. The package is designed to simplify common tasks in categorical data analysis, making it easier to work with factors in a flexible and efficient manner.

Maintained by Kai Guo. Last updated 5 months ago.

6.6 match 2 stars 4.60 score 4 scripts

tidyverse

dbplyr:A 'dplyr' Back End for Databases

A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.

Maintained by Hadley Wickham. Last updated 3 months ago.

database

1.5 match 481 stars 19.72 score 5.2k scripts 736 dependents

poissonconsulting

mcmcr:Manipulate MCMC Samples

Functions and classes to store, manipulate and summarise Monte Carlo Markov Chain (MCMC) samples. For more information see Brooks et al. (2011) <isbn:978-1-4200-7941-8>.

Maintained by Joe Thorley. Last updated 2 months ago.

coda mcmc

3.9 match 17 stars 7.66 score 111 scripts 10 dependents

bioc

cummeRbund:Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

Maintained by Loyal A. Goff. Last updated 5 months ago.

highthroughputsequencing highthroughputsequencingdata rnaseq rnaseqdata geneexpression differentialexpression infrastructure dataimport datarepresentation visualization bioinformatics clustering multiplecomparisons qualitycontrol

4.9 match 5.92 score 209 scripts

mplex

multigraph:Plot and Manipulate Multigraphs

Functions to plot and manipulate multigraphs, signed and valued graphs, bipartite graphs, multilevel graphs, and Cayley graphs with various layout options.

Maintained by Antonio Rivero Ostoic. Last updated 2 months ago.

bipartite-graphs bipartite-network graph graph-visualization network-analysis network-visualization plot

5.9 match 22 stars 4.97 score 14 scripts

ropensci

datapack:A Flexible Container to Transport and Manipulate Data and Associated Resources

Provides a flexible container to transport and manipulate complex sets of data. These data may consist of multiple data files and associated meta data and ancillary files. Individual data objects have associated system level meta data, and data files are linked together using the OAI-ORE standard resource map which describes the relationships between the files. The OAI- ORE standard is described at <https://www.openarchives.org/ore/>. Data packages can be serialized and transported as structured files that have been created following the BagIt specification. The BagIt specification is described at <https://tools.ietf.org/html/draft-kunze-bagit-08>.

Maintained by Matthew B. Jones. Last updated 3 years ago.

3.4 match 44 stars 8.56 score 195 scripts 4 dependents

ropensci

taxlist:Handling Taxonomic Lists

Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (<https://www.synbiosys.alterra.nl/turboveg/>) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.

Maintained by Miguel Alvarez. Last updated 6 months ago.

4.0 match 12 stars 7.07 score 81 scripts 2 dependents

evolecolgroup

pastclim:Manipulate Time Series of Climate Reconstructions

Methods to easily extract and manipulate climate reconstructions for ecological and anthropological analyses, as described in Leonardi et al. (2023) <doi:10.1111/ecog.06481>. The package includes datasets of palaeoclimate reconstructions, present observations, and future projections from multiple climate models.

Maintained by Andrea Manica. Last updated 3 days ago.

climate-data paleoclimate species-distribution-modelling

3.5 match 38 stars 8.12 score 49 scripts

cbailiss

basictabler:Construct Rich Tables for Output to 'HTML'/'Excel'

Easily create tables from data frames/matrices. Create/manipulate tables row-by-row, column-by-column or cell-by-cell. Use common formatting/styling to output rich tables as 'HTML', 'HTML widgets' or to 'Excel'.

Maintained by Christopher Bailiss. Last updated 4 years ago.

html htmlwidget tables visualization

4.0 match 37 stars 7.09 score 94 scripts

ropensci

eph:Argentina's Permanent Household Survey Data and Manipulation Utilities

Tools to download and manipulate the Permanent Household Survey from Argentina (EPH is the Spanish acronym for Permanent Household Survey). e.g: get_microdata() for downloading the datasets, get_poverty_lines() for downloading the official poverty baskets, calculate_poverty() for the calculation of stating if a household is in poverty or not, following the official methodology. organize_panels() is used to concatenate observations from different periods, and organize_labels() adds the official labels to the data. The implemented methods are based on INDEC (2016) <http://www.estadistica.ec.gba.gov.ar/dpe/images/SOCIEDAD/EPH_metodologia_22_pobreza.pdf>. As this package works with the argentinian Permanent Household Survey and its main audience is from this country, the documentation was written in Spanish.

Maintained by Carolina Pradier. Last updated 7 months ago.

eph indec mercado-de-trabajo rstatses

3.4 match 59 stars 8.38 score 255 scripts

immunomind

immunarch:Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.

Maintained by Vadim I. Nazarov. Last updated 12 months ago.

airr-analysis b-cell-receptor bcr bcr-repertoire bioinformatics ig ig-repertoire immune-repertoire immune-repertoire-analysis immune-repertoire-data immunoglobulin immunoinformatics immunology rep-seq repertoire-analysis single-cell single-cell-analysis t-cell-receptor tcr tcr-repertoire cpp

2.9 match 315 stars 9.49 score 203 scripts

bioc

GenomicTuples:Representation and Manipulation of Genomic Tuples

GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.

Maintained by Peter Hickey. Last updated 4 months ago.

infrastructure datarepresentation sequencing cpp

5.0 match 4 stars 5.48 score 7 scripts

jibarozzo

nplyr:A Grammar of Nested Data Manipulation

Provides functions for manipulating nested data frames in a list-column using 'dplyr' <https://dplyr.tidyverse.org/> syntax. Rather than unnesting, then manipulating a data frame, 'nplyr' allows users to manipulate each nested data frame directly. 'nplyr' is a wrapper for 'dplyr' functions that provide tools for common data manipulation steps: filtering rows, selecting columns, summarising grouped data, among others.

Maintained by Bolívar Aponte Rolón. Last updated 1 months ago.

4.1 match 120 stars 6.56 score 1 dependents

muschellij2

neurobase:'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects

Base package for 'Neuroconductor', which includes many helper functions that interact with objects of class 'nifti', implemented by package 'oro.nifti', for reading/writing and also other manipulation functions.

Maintained by John Muschelli. Last updated 1 months ago.

3.2 match 5 stars 8.49 score 486 scripts 7 dependents

pik-piam

lucode2:Code Manipulation and Analysis Tools

A collection of tools which allow to manipulate and analyze code.

Maintained by Jan Philipp Dietrich. Last updated 23 days ago.

3.7 match 7.22 score 364 scripts 8 dependents

prioritizr

prioritizr:Systematic Conservation Prioritization in R

Systematic conservation prioritization using mixed integer linear programming (MILP). It provides a flexible interface for building and solving conservation planning problems. Once built, conservation planning problems can be solved using a variety of commercial and open-source exact algorithm solvers. By using exact algorithm solvers, solutions can be generated that are guaranteed to be optimal (or within a pre-specified optimality gap). Furthermore, conservation problems can be constructed to optimize the spatial allocation of different management actions or zones, meaning that conservation practitioners can identify solutions that benefit multiple stakeholders. To solve large-scale or complex conservation planning problems, users should install the Gurobi optimization software (available from <https://www.gurobi.com/>) and the 'gurobi' R package (see Gurobi Installation Guide vignette for details). Users can also install the IBM CPLEX software (<https://www.ibm.com/products/ilog-cplex-optimization-studio/cplex-optimizer>) and the 'cplexAPI' R package (available at <https://github.com/cran/cplexAPI>). Additionally, the 'rcbc' R package (available at <https://github.com/dirkschumacher/rcbc>) can be used to generate solutions using the CBC optimization software (<https://github.com/coin-or/Cbc>). For further details, see Hanson et al. (2025) <doi:10.1111/cobi.14376>.

Maintained by Richard Schuster. Last updated 11 days ago.

biodiversity conservation conservation-planner optimization prioritization solver spatial cpp

2.3 match 124 stars 11.82 score 584 scripts 2 dependents

ediorg

ecocomDP:Tools to Create, Use, and Convert ecocomDP Data

Work with the Ecological Community Data Design Pattern. 'ecocomDP' is a flexible data model for harmonizing ecological community surveys, in a research question agnostic format, from source data published across repositories, and with methods that keep the derived data up-to-date as the underlying sources change. Described in O'Brien et al. (2021), <doi:10.1016/j.ecoinf.2021.101374>.

Maintained by Colin Smith. Last updated 7 months ago.

3.2 match 32 stars 8.22 score 77 scripts

dmurdoch

rgl:3D Visualization Using OpenGL

Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.

Maintained by Duncan Murdoch. Last updated 2 months ago.

graphics opengl rgl webgl libglu libglvnd libpng libx11 freetype cpp

1.5 match 91 stars 17.49 score 7.3k scripts 300 dependents

spatstat

spatstat.utils:Utility Functions for 'spatstat'

Contains utility functions for the 'spatstat' family of packages which may also be useful for other purposes.

Maintained by Adrian Baddeley. Last updated 2 days ago.

spatial-analysis spatial-data spatstat

2.3 match 5 stars 11.66 score 134 scripts 248 dependents

bioc

biodb:biodb, a library and a development framework for connecting to chemical and biological databases

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

Maintained by Pierrick Roger. Last updated 5 months ago.

software infrastructure dataimport kegg biology cheminformatics chemistry databases cpp

3.3 match 11 stars 7.85 score 24 scripts 6 dependents

bioc

MultiAssayExperiment:Software for the integration of multi-omics experiments in Bioconductor

Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.

Maintained by Marcel Ramos. Last updated 2 months ago.

infrastructure datarepresentation bioconductor bioconductor-package genomics nci-itcr tcga u24ca289073

1.8 match 71 stars 14.95 score 670 scripts 127 dependents

bioc

SplicingGraphs:Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.

Maintained by H. Pagès. Last updated 5 months ago.

genetics annotation datarepresentation visualization sequencing rnaseq geneexpression alternativesplicing transcription immunooncology bioconductor-package

5.0 match 2 stars 5.26 score 8 scripts

ropensci

phylogram:Dendrograms for Evolutionary Analysis

Contains functions for developing phylogenetic trees as deeply-nested lists ("dendrogram" objects). Enables bi-directional conversion between dendrogram and "phylo" objects (see Paradis et al (2004) <doi:10.1093/bioinformatics/btg412>), and features several tools for command-line tree manipulation and import/export via Newick parenthetic text.

Maintained by Shaun Wilkinson. Last updated 5 years ago.

peer-reviewed

3.0 match 11 stars 8.53 score 228 scripts 9 dependents

r-quantities

units:Measurement Units for R Vectors

Support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. Compatible with the POSIXct, Date and difftime classes. Uses the UNIDATA udunits library and unit database for unit compatibility checking and conversion. Documentation about 'units' is provided in the paper by Pebesma, Mailund & Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a vignette; see 'citation("units")' for details.

Maintained by Edzer Pebesma. Last updated 4 days ago.

udunits cpp

1.5 match 181 stars 17.28 score 3.3k scripts 1.2k dependents

bayesiandemography

poputils:Demographic Analysis and Data Manipulation

Perform tasks commonly encountered when preparing and analysing demographic data. Some functions are intended for end users, and others for developers. Includes functions for working with life tables.

Maintained by John Bryant. Last updated 6 months ago.

cpp

4.6 match 5.57 score 49 scripts 1 dependents

data-cleaning

editrules:Parsing, Applying, and Manipulating Data Cleaning Rules

Please note: active development has moved to packages 'validate' and 'errorlocate'. Facilitates reading and manipulating (multivariate) data restrictions (edit rules) on numerical and categorical data. Rules can be defined with common R syntax and parsed to an internal (matrix-like format). Rules can be manipulated with variable elimination and value substitution methods, allowing for feasibility checks and more. Data can be tested against the rules and erroneous fields can be found based on Fellegi and Holt's generalized principle. Rules dependencies can be visualized with using the 'igraph' package.

Maintained by Edwin de Jonge. Last updated 9 months ago.

3.7 match 22 stars 6.97 score 140 scripts 1 dependents

inseefrlab

rjdworkspace:Manipulate 'JDemetra+' Workspaces

Set of tools to manipulate the 'JDemetra+' workspaces. Based on the 'RJDemetra' package (which interfaces with version 2 of the 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal adjustment software officially recommended to the members of the European Statistical System (ESS) and the European System of Central Banks). This package provides access to additional workspace manipulation functions such as metadata manipulation, raw paths and wrangling of several workspaces simultaneously. These additional functionalities are useful as part of a CVS data production chain.

Maintained by Tanguy Barthelemy. Last updated 2 months ago.

jdemetra rjdemetra workspace-management openjdk

6.3 match 1 stars 4.08 score 2 scripts

quantilma

quantdates:Manipulate Dates for Finance

Functions to manipulate dates and count days for quantitative finance analysis. The 'quantdates' package considers leap, holidays and business days for relevant calendars in a financial context to simplify quantitative finance calculations, consistent with International Swaps and Derivatives Association (ISDA) (2006) <https://www.isda.org/book/2006-isda-definitions/> regulations.

Maintained by Juan Pablo Bermudez. Last updated 9 months ago.

dates finance quantitative-finance

5.3 match 2 stars 4.78 score 3 scripts 1 dependents

itsleeds

od:Manipulate and Map Origin-Destination Data

The aim of 'od' is to provide tools and example datasets for working with origin-destination ('OD') datasets of the type used to describe aggregate urban mobility patterns (Carey et al. 1981) <doi:10.1287/trsc.15.1.32>. The package builds on functions for working with 'OD' data in the package 'stplanr', (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053> with a focus on computational efficiency and support for the 'sf' class system (Pebesma 2018) <doi:10.32614/RJ-2018-009>. With few dependencies and a simple class system based on data frames, the package is intended to facilitate efficient analysis of 'OD' datasets and to provide a place for developing new functions. The package enables the creation and analysis of geographic entities representing large scale mobility patterns, from daily travel between zones in cities to migration between countries.

Maintained by Robin Lovelace. Last updated 5 months ago.

3.0 match 33 stars 8.50 score 96 scripts 6 dependents

dbosak01

procs:Recreates Some 'SAS®' Procedures in 'R'

Contains functions to simulate the most commonly used 'SAS®' procedures. Specifically, the package aims to simulate the functionality of 'proc freq', 'proc means', 'proc ttest', 'proc reg', 'proc transpose', 'proc sort', and 'proc print'. The simulation will include recreating all statistics with the highest fidelity possible.

Maintained by David Bosak. Last updated 10 months ago.

3.3 match 6 stars 7.57 score 37 scripts 2 dependents

pharmaverse

tidytlg:Create TLGs using the 'tidyverse'

Generate tables, listings, and graphs (TLG) using 'tidyverse.' Tables can be created functionally, using a standard TLG process, or by specifying table and column metadata to create generic analysis summaries. The 'envsetup' package can also be leveraged to create environments for table creation.

Maintained by Konrad Pagacz. Last updated 9 months ago.

3.1 match 33 stars 8.07 score 22 scripts

poissonconsulting

term:Create, Manipulate and Query Parameter Terms

Creates, manipulates, queries and repairs vectors of parameter terms. Parameter terms are the labels used to reference values in vectors, matrices and arrays. They represent the names in coefficient tables and the column names in 'mcmc' and 'mcmc.list' objects.

Maintained by Joe Thorley. Last updated 2 months ago.

coefficients mcmc term

3.5 match 10 stars 7.15 score 15 scripts 13 dependents

reedacartwright

rbedrock:Analysis and Manipulation of Data from Minecraft Bedrock Edition

Implements an interface to Minecraft (Bedrock Edition) worlds. Supports the analysis and management of these worlds and game saves.

Maintained by Reed Cartwright. Last updated 18 days ago.

zlib cpp

4.8 match 43 stars 5.24 score 3 scripts

bioc

xcms:LC-MS and GC-MS Data Analysis

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

Maintained by Steffen Neumann. Last updated 3 days ago.

immunooncology massspectrometry metabolomics bioconductor feature-detection mass-spectrometry peak-detection cpp

1.8 match 196 stars 14.31 score 984 scripts 11 dependents

pasraia

RRphylo:Phylogenetic Ridge Regression Methods for Comparative Studies

Functions for phylogenetic analysis (Castiglione et al., 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.

Maintained by Silvia Castiglione. Last updated 7 months ago.

3.3 match 10 stars 7.48 score 83 scripts

benmbutler

powdR:Full Pattern Summation of X-Ray Powder Diffraction Data

Full pattern summation of X-ray powder diffraction data as described in Chipera and Bish (2002) <doi:10.1107/S0021889802017405> and Butler and Hillier (2021) <doi:10.1016/j.cageo.2020.104662>. Derives quantitative estimates of crystalline and amorphous phase concentrations in complex mixtures.

Maintained by Benjamin Butler. Last updated 3 years ago.

4.5 match 12 stars 5.56 score 30 scripts

sciviews

svUnit:'SciViews' - Unit, Integration and System Testing

A complete unit test system.

Maintained by Philippe Grosjean. Last updated 3 years ago.

sciviews testing-tools

3.0 match 3 stars 8.07 score 72 scripts 28 dependents

matthieugomez

statar:Tools Inspired by 'Stata' to Manipulate Tabular Data

A set of tools inspired by 'Stata' to explore data.frames ('summarize', 'tabulate', 'xtile', 'pctile', 'binscatter', elapsed quarters/month, lead/lag).

Maintained by Matthieu Gomez. Last updated 2 years ago.

2.9 match 54 stars 8.40 score 226 scripts 1 dependents

echasnovski

comperes:Manage Competition Results

Tools for storing and managing competition results. Competition is understood as a set of games in which players gain some abstract scores. There are two ways for storing results: in long (one row per game-player) and wide (one row per game with fixed amount of players) formats. This package provides functions for creation and conversion between them. Also there are functions for computing their summary and Head-to-Head values for players. They leverage grammar of data manipulation from 'dplyr'.

Maintained by Evgeni Chasnovski. Last updated 2 years ago.

3.8 match 8 stars 6.28 score 40 scripts 1 dependents

r-lib

callr:Call R from R

It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.

Maintained by Gábor Csárdi. Last updated 22 days ago.

1.6 match 300 stars 15.28 score 289 scripts 1.2k dependents

truecluster

ff:Memory-Efficient Storage of Large Data on Disk and Fast Access Functions

The ff package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section (pagesize) in main memory - the effective virtual memory consumption per ff object. ff supports R's standard atomic data types 'double', 'logical', 'raw' and 'integer' and non-standard atomic types boolean (1 bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned), single (4 byte float with NAs). For example 'quad' allows efficient storage of genomic data as an 'A','T','G','C' factor. The unsigned types support 'circular' arithmetic. There is also support for close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and custom close-to-atomic types. ff not only has native C-support for vectors, matrices and arrays with flexible dimorder (major column-order, major row-order and generalizations for arrays). There is also a ffdf class not unlike data.frames and import/export filters for csv files. ff objects store raw data in binary flat files in native encoding, and complement this with metadata stored in R as physical and virtual attributes. ff objects have well-defined hybrid copying semantics, which gives rise to certain performance improvements through virtualization. ff objects can be stored and reopened across R sessions. ff files can be shared by multiple ff R objects (using different data en/de-coding schemes) in the same process or from multiple R processes to exploit parallelism. A wide choice of finalizer options allows to work with 'permanent' files as well as creating/removing 'temporary' ff files completely transparent to the user. On certain OS/Filesystem combinations, creating the ff files works without notable delay thanks to using sparse file allocation. Several access optimization techniques such as Hybrid Index Preprocessing and Virtualization are implemented to achieve good performance even with large datasets, for example virtual matrix transpose without touching a single byte on disk. Further, to reduce disk I/O, 'logicals' and non-standard data types get stored native and compact on binary flat files i.e. logicals take up exactly 2 bits to represent TRUE, FALSE and NA. Beyond basic access functions, the ff package also provides compatibility functions that facilitate writing code for ff and ram objects and support for batch processing on ff objects (e.g. as.ram, as.ff, ffapply). ff interfaces closely with functionality from package 'bit': chunked looping, fast bit operations and coercions between different objects that can store subscript information ('bit', 'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows to work interactively with selections of large datasets and quickly modify selection criteria. Further high-performance enhancements can be made available upon request.

Maintained by Jens Oehlschlägel. Last updated 2 months ago.

cpp

2.0 match 27 stars 12.01 score 764 scripts 71 dependents

sfirke

janitor:Simple Tools for Examining and Cleaning Dirty Data

The main janitor functions can: perfectly format data.frame column names; provide quick counts of variable combinations (i.e., frequency tables and crosstabs); and explore duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and-report functions approximate popular features of SPSS and Microsoft Excel. This package follows the principles of the "tidyverse" and works well with the pipe function %>%. janitor was built with beginning-to-intermediate R users in mind and is optimized for user-friendliness.

Maintained by Sam Firke. Last updated 3 months ago.

data-analysis data-cleaning data-science dirty-data excel pivot-tables spss tabulations tidyverse

1.3 match 1.4k stars 19.15 score 35k scripts 231 dependents

bioc

GenomicDataCommons:NIH / NCI Genomic Data Commons Access

Programmatically access the NIH / NCI Genomic Data Commons RESTful service.

Maintained by Sean Davis. Last updated 1 months ago.

dataimport sequencing api-client bioconductor bioinformatics cancer core-services data-science genomics nci tcga vignette

2.0 match 87 stars 11.94 score 238 scripts 12 dependents

ropensci

taxa:Classes for Storing and Manipulating Taxonomic Data

Provides classes for storing and manipulating taxonomic data. Most of the classes can be treated like base R vectors (e.g. can be used in tables as columns and can be named). Vectorized classes can store taxon names and authorities, taxon IDs from databases, taxon ranks, and other types of information. More complex classes are provided to store taxonomic trees and user-defined data associated with them.

Maintained by Zachary Foster. Last updated 1 years ago.

taxonomy biology hierarchy data-cleaning taxon

3.5 match 48 stars 6.80 score 217 scripts

open-eo

openeo:Client Interface for 'openEO' Servers

Access data and processing functionalities of 'openEO' compliant back-ends in R.

Maintained by Florian Lahn. Last updated 2 months ago.

openeo openeo-user

2.8 match 64 stars 8.65 score 128 scripts

fcharte

mldr:Exploratory Data Analysis and Manipulation of Multi-Label Data Sets

Exploratory data analysis and manipulation functions for multi- label data sets along with an interactive Shiny application to ease their use.

Maintained by David Charte. Last updated 5 years ago.

3.3 match 23 stars 7.07 score 168 scripts 2 dependents

r-causal

ggdag:Analyze and Create Elegant Directed Acyclic Graphs

Tidy, analyze, and plot directed acyclic graphs (DAGs). 'ggdag' is built on top of 'dagitty', an R package that uses the 'DAGitty' web tool (<https://dagitty.net/>) for creating and analyzing DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty' objects using 'ggplot2' and 'ggraph', as well as common analytic and graphical functions, such as determining adjustment sets and node relationships.

Maintained by Malcolm Barrett. Last updated 8 months ago.

causal-inference dag ggplot-extension

2.0 match 443 stars 11.78 score 1.8k scripts 5 dependents

eglenn

acs:Download, Manipulate, and Present American Community Survey and Decennial Data from the US Census

Provides a general toolkit for downloading, managing, analyzing, and presenting data from the U.S. Census (<https://www.census.gov/data/developers/data-sets.html>), including SF1 (Decennial short-form), SF3 (Decennial long-form), and the American Community Survey (ACS). Confidence intervals provided with ACS data are converted to standard errors to be bundled with estimates in complex acs objects. Package provides new methods to conduct standard operations on acs objects and present/plot data in statistically appropriate ways.

Maintained by Ezra Haber Glenn. Last updated 6 years ago.

4.4 match 11 stars 5.33 score 430 scripts 3 dependents

bioc

RedeR:Interactive visualization and manipulation of nested networks

RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of nested networks. Graph, node, and edge attributes can be configured using either graphical or command-line methods, following igraph syntax rules.

Maintained by Mauro Castro. Last updated 5 months ago.

gui graphandnetwork network networkenrichment networkinference software systemsbiology

3.5 match 6.65 score 107 scripts 7 dependents

ropengov

geofi:Access Finnish Geospatial Data

Designed to simplify geospatial data access from the Statistics Finland Web Feature Service API <https://geo.stat.fi/geoserver/index.html>, the geofi package offers researchers and analysts a set of tools to obtain and harmonize administrative spatial data for a wide range of applications, from urban planning to environmental research. The package contains annually updated time series of municipality key datasets that can be used for data aggregation and language translations.

Maintained by Markus Kainu. Last updated 1 months ago.

ropengov ggplot2

2.9 match 20 stars 8.17 score 61 scripts

friendly

matlib:Matrix Functions for Teaching and Learning Linear Algebra and Multivariate Statistics

A collection of matrix functions for teaching and learning matrix linear algebra as used in multivariate statistical methods. Many of these functions are designed for tutorial purposes in learning matrix algebra ideas using R. In some cases, functions are provided for concepts available elsewhere in R, but where the function call or name is not obvious. In other cases, functions are provided to show or demonstrate an algorithm. In addition, a collection of functions are provided for drawing vector diagrams in 2D and 3D and for rendering matrix expressions and equations in LaTeX.

Maintained by Michael Friendly. Last updated 2 days ago.

diagrams linear-equations matrix matrix-functions matrix-visualizer vector vignette

1.8 match 65 stars 12.89 score 900 scripts 11 dependents

ndphillips

FFTrees:Generate, Visualise, and Evaluate Fast-and-Frugal Decision Trees

Create, visualize, and test fast-and-frugal decision trees (FFTs) using the algorithms and methods described by Phillips, Neth, Woike & Gaissmaier (2017), <doi:10.1017/S1930297500006239>. FFTs are simple and transparent decision trees for solving binary classification problems. FFTs can be preferable to more complex algorithms because they require very little information, are easy to understand and communicate, and are robust against overfitting.

Maintained by Hansjoerg Neth. Last updated 5 months ago.

2.4 match 135 stars 9.58 score 144 scripts

colinfay

attempt:Tools for Defensive Programming

Tools for defensive programming, inspired by 'purrr' mappers and based on 'rlang'.'attempt' extends and facilitates defensive programming by providing a consistent grammar, and provides a set of easy to use functions for common tests and conditions. 'attempt' only depends on 'rlang', and focuses on speed, so it can be easily integrated in other functions and used in data analysis.

Maintained by Colin Fay. Last updated 7 months ago.

2.0 match 126 stars 11.57 score 101 scripts 86 dependents

discoleo

Rpdb:Read, Write, Visualize and Manipulate PDB Files

Provides tools to read, write, visualize Protein Data Bank (PDB) files and perform some structural manipulations.

Maintained by Leonard Mada. Last updated 26 days ago.

5.2 match 4.43 score 68 scripts

joshobrien

rasterDT:Fast Raster Summary and Manipulation

Fast alternatives to several relatively slow 'raster' package functions. For large rasters, the functions run from 5 to approximately 100 times faster than the 'raster' package functions they replace. The 'fasterize' package, on which one function in this package depends, includes an implementation of the scan line algorithm attributed to Wylie et al. (1967) <doi:10.1145/1465611.1465619>.

Maintained by Joshua OBrien. Last updated 2 years ago.

5.0 match 27 stars 4.61 score 8 scripts 1 dependents

datastorm-open

visNetwork:Network Visualization using 'vis.js' Library

Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.

Maintained by Benoit Thieurmel. Last updated 2 years ago.

1.5 match 549 stars 15.14 score 4.1k scripts 195 dependents

ropensci

jqr:Client for 'jq', a 'JSON' Processor

Client for 'jq', a 'JSON' processor (<https://jqlang.github.io/jq/>), written in C. 'jq' allows the following with 'JSON' data: index into, parse, do calculations, cut up and filter, change key names and values, perform conditionals and comparisons, and more.

Maintained by Jeroen Ooms. Last updated 3 months ago.

jq json

2.3 match 144 stars 10.04 score 95 scripts 28 dependents

jeswheel

panelPomp:Inference for Panel Partially Observed Markov Processes

Data analysis based on panel partially-observed Markov process (PanelPOMP) models. To implement such models, simulate them and fit them to panel data, 'panelPomp' extends some of the facilities provided for time series data by the 'pomp' package. Implemented methods include filtering (panel particle filtering) and maximum likelihood estimation (Panel Iterated Filtering) as proposed in Breto, Ionides and King (2020) "Panel Data Analysis via Mechanistic Models" <doi:10.1080/01621459.2019.1604367>.

Maintained by Jesse Wheeler. Last updated 3 months ago.

3.8 match 5.91 score 45 scripts

mkoohafkan

arcpy:Interface to 'ArcGIS' 'Python' Modules

An interface to the 'ArcGIS' 'arcpy' and 'arcgis' 'python' API <https://pro.arcgis.com/en/pro-app/latest/arcpy/get-started/arcgis-api-for-python.htm>. Provides various tools for installing and configuring a 'Conda' environment for accessing 'ArcGIS' geoprocessing functions. Helper functions for manipulating and converting 'ArcGIS' objects from R are also provided.

Maintained by Michael Koohafkan. Last updated 7 months ago.

4.3 match 9 stars 5.26 score 9 scripts

ouhscbbmc

REDCapR:Interaction Between R and REDCap

Encapsulates functions to streamline calls from R to the REDCap API. REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The Application Programming Interface (API) offers an avenue to access and modify data programmatically, improving the capacity for literate and reproducible programming.

Maintained by Will Beasley. Last updated 2 months ago.

redcap redcap-api

1.8 match 118 stars 12.36 score 438 scripts 6 dependents

roux-ohdsi

allofus:Interface for 'All of Us' Researcher Workbench

Streamline use of the 'All of Us' Researcher Workbench (<https://www.researchallofus.org/data-tools/workbench/>)with tools to extract and manipulate data from the 'All of Us' database. Increase interoperability with the Observational Health Data Science and Informatics ('OHDSI') tool stack by decreasing reliance of 'All of Us' tools and allowing for cohort creation via 'Atlas'. Improve reproducible and transparent research using 'All of Us'.

Maintained by Rob Cavanaugh. Last updated 4 months ago.

3.1 match 16 stars 7.19 score 30 scripts

magnusdv

pedtools:Creating and Working with Pedigrees and Marker Data

A comprehensive collection of tools for creating, manipulating and visualising pedigrees and genetic marker data. Pedigrees can be read from text files or created on the fly with built-in functions. A range of utilities enable modifications like adding or removing individuals, breaking loops, and merging pedigrees. An online tool for creating pedigrees interactively, based on 'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>. 'pedtools' is the hub of the 'pedsuite', a collection of packages for pedigree analysis. A detailed presentation of the 'pedsuite' is given in the book 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).

Maintained by Magnus Dehli Vigeland. Last updated 2 months ago.

2.5 match 25 stars 8.83 score 60 scripts 18 dependents

matthewheun

RCLabels:Manipulate Matrix Row and Column Labels with Ease

Functions to assist manipulation of matrix row and column labels for all types of matrix mathematics where row and column labels are to be respected.

Maintained by Matthew Heun. Last updated 11 days ago.

4.6 match 1 stars 4.78 score 5 scripts 2 dependents

bioc

S4Arrays:Foundation of array-like containers in Bioconductor

The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects).

Maintained by Hervé Pagès. Last updated 1 months ago.

infrastructure datarepresentation bioconductor-package core-package

2.0 match 5 stars 10.99 score 8 scripts 1.2k dependents