Showing 40 of total 40 results (show query)
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 25 days ago.
4.8k stars 24.68 score 659k scripts 7.8k dependents
plotly
plotly:Create Interactive Web Graphics via 'plotly.js'
Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Maintained by Carson Sievert. Last updated 3 months ago.
d3jsdata-visualizationggplot2javascriptplotlyshinywebgl
2.6k stars 19.43 score 93k scripts 797 dependents
bioc
clusterProfiler:A universal enrichment tool for interpreting omics data
This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions.
Maintained by Guangchuang Yu. Last updated 4 months ago.
annotationclusteringgenesetenrichmentgokeggmultiplecomparisonpathwaysreactomevisualizationenrichment-analysisgsea
1.1k stars 17.03 score 11k scripts 48 dependents
kassambara
ggpubr:'ggplot2' Based Publication Ready Plots
The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.
Maintained by Alboukadel Kassambara. Last updated 2 years ago.
1.2k stars 16.68 score 65k scripts 409 dependentskassambara
rstatix:Pipe-Friendly Framework for Basic Statistical Tests
Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy, for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. The output of each test is automatically transformed into a tidy data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs (repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs. It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and 'Cramer V' for the association between categorical variables. The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.
Maintained by Alboukadel Kassambara. Last updated 2 years ago.
458 stars 15.27 score 11k scripts 432 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 3 months ago.
data-modeldata-warehousingdatawarehousingdbidbplyrrelational-databases
511 stars 14.81 score 410 scripts 8 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 2 months ago.
graph-algorithmsgraph-manipulationigraphnetwork-analysistidyversecpp
553 stars 14.74 score 4.6k scripts 136 dependents
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 2 months ago.
215 stars 13.88 score 1.8k scripts 15 dependents
dieghernan
tidyterra:'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects
Extension of the 'tidyverse' for 'SpatRaster' and 'SpatVector' objects of the 'terra' package. It includes also new 'geom_' functions that provide a convenient way of visualizing 'terra' objects with 'ggplot2'.
Maintained by Diego Hernangómez. Last updated 4 days ago.
terraggplot-extensionr-spatialrspatial
190 stars 13.59 score 1.9k scripts 25 dependentsbioc
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 10 days ago.
infrastructuredatarepresentationworkflowstepcoveragebioconductordata-analysisdplyrgenomic-rangesgenomicstidy-data
144 stars 12.66 score 1.9k scripts 20 dependents
billdenney
PKNCA:Perform Pharmacokinetic Non-Compartmental Analysis
Compute standard Non-Compartmental Analysis (NCA) parameters for typical pharmacokinetic analyses and summarize them.
Maintained by Bill Denney. Last updated 29 days ago.
ncanoncompartmental-analysispharmacokinetics
73 stars 12.61 score 214 scripts 4 dependents
johncoene
echarts4r:Create Interactive Graphs with 'Echarts JavaScript' Version 5
Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes 36 chart types, themes, 'Shiny' proxies and animations.
Maintained by David Munoz Tord. Last updated 15 days ago.
echartshacktoberfesthtmlwidgethtmlwidgetsvisualization
603 stars 11.45 score 1.3k scripts 11 dependents
markfairbanks
tidytable:Tidy Interface to 'data.table'
A tidy interface to 'data.table', giving users the speed of 'data.table' while using tidyverse-like syntax.
Maintained by Mark Fairbanks. Last updated 2 months ago.
460 stars 11.39 score 732 scripts 11 dependents
uupharmacometrics
xpose:Diagnostics for Pharmacometric Models
Diagnostics for non-linear mixed-effects (population) models from 'NONMEM' <https://www.iconplc.com/solutions/technologies/nonmem/>. 'xpose' facilitates data import, creation of numerical run summary and provide 'ggplot2'-based graphics for data exploration and model diagnostics.
Maintained by Benjamin Guiastrennec. Last updated 3 months ago.
diagnosticsggplot2nonmempharmacometricsxpose
62 stars 11.02 score 183 scripts 6 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-rdata-manipulationgrammar
342 stars 10.79 score 156 scripts 27 dependents
mitchelloharawild
vitae:Curriculum Vitae for R Markdown
Provides templates and functions to simplify the production and maintenance of curriculum vitae.
Maintained by Mitchell OHara-Wild. Last updated 10 months ago.
1.2k stars 10.78 score 556 scripts
jmsigner
amt:Animal Movement Tools
Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate home ranges, track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses, and simulation of space-use from fitted step-selection functions.
Maintained by Johannes Signer. Last updated 5 months ago.
41 stars 10.54 score 418 scripts
elbersb
tidylog:Logging for 'dplyr' and 'tidyr' Functions
Provides feedback about 'dplyr' and 'tidyr' operations.
Maintained by Benjamin Elbers. Last updated 10 months ago.
dplyrtidyrtidyversewrapper-functions
593 stars 10.23 score 1.7k scriptsbioc
MicrobiotaProcess:A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).
Maintained by Shuangbin Xu. Last updated 5 months ago.
visualizationmicrobiomesoftwaremultiplecomparisonfeatureextractionmicrobiome-analysismicrobiome-data
183 stars 9.70 score 126 scripts 1 dependentsbioc
tidybulk:Brings transcriptomics to the tidyverse
This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.
Maintained by Stefano Mangiola. Last updated 11 days ago.
assaydomaininfrastructurernaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomicsbioconductorbulk-transcriptional-analysesdeseq2differential-expressionedgerensembl-idsentrezgene-symbolsgseamds-dimensionspcapiperedundancytibbletidytidy-datatidyversetranscriptstsne
171 stars 9.57 score 172 scripts 1 dependents
adibender
pammtools:Piece-Wise Exponential Additive Mixed Modeling Tools for Survival Analysis
The Piece-wise exponential (Additive Mixed) Model (PAMM; Bender and others (2018) <doi: 10.1177/1471082X17748083>) is a powerful model class for the analysis of survival (or time-to-event) data, based on Generalized Additive (Mixed) Models (GA(M)Ms). It offers intuitive specification and robust estimation of complex survival models with stratified baseline hazards, random effects, time-varying effects, time-dependent covariates and cumulative effects (Bender and others (2019)), as well as support for left-truncated data as well as competing risks, recurrent events and multi-state settings. pammtools provides tidy workflow for survival analysis with PAMMs, including data simulation, transformation and other functions for data preprocessing and model post-processing as well as visualization.
Maintained by Andreas Bender. Last updated 5 days ago.
additive-modelspammpammtoolspiece-wise-exponentialsurvival-analysis
48 stars 9.32 score 310 scripts 8 dependents
atlasoflivingaustralia
galah:Biodiversity Data from the GBIF Node Network
The Global Biodiversity Information Facility ('GBIF', <https://www.gbif.org>) sources data from an international network of data providers, known as 'nodes'. Several of these nodes - the "living atlases" (<https://living-atlases.gbif.org>) - maintain their own web services using software originally developed by the Atlas of Living Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community to directly access data and resources hosted by 'GBIF' and its partner nodes.
Maintained by Martin Westgate. Last updated 2 months ago.
43 stars 9.17 score 275 scripts 1 dependents
bupaverse
bupaR:Business Process Analysis in R
Comprehensive Business Process Analysis toolkit. Creates S3-class for event log objects, and related handler functions. Imports related packages for filtering event data, computation of descriptive statistics, handling of 'Petri Net' objects and visualization of process maps. See also packages 'edeaR','processmapR', 'eventdataR' and 'processmonitR'.
Maintained by Gert Janssenswillen. Last updated 2 years ago.
57 stars 9.06 score 389 scripts 11 dependents
somalogic
SomaDataIO:Input/Output 'SomaScan' Data
Load and export 'SomaScan' data via the 'Standard BioTools, Inc.' structured text file called an ADAT ('*.adat'). For file format see <https://github.com/SomaLogic/SomaLogic-Data/blob/main/README.md>. The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory.
Maintained by Caleb Scheidel. Last updated 2 months ago.
adatproteomicsproteomics-data-analysissomascan
26 stars 7.71 score 132 scripts
hadley
ggvis:Interactive Grammar of Graphics
An implementation of an interactive grammar of graphics, taking the best parts of 'ggplot2', combining them with the reactive framework of 'shiny' and drawing web graphics using 'vega'.
Maintained by Hadley Wickham. Last updated 1 years ago.
1 stars 7.02 score 2.3k scripts 11 dependents
statisfactions
simpr:Flexible 'Tidyverse'-Friendly Simulations
A general, 'tidyverse'-friendly framework for simulation studies, design analysis, and power analysis. Specify data generation, define varying parameters, generate data, fit models, and tidy model results in a single pipeline, without needing loops or custom functions.
Maintained by Ethan Brown. Last updated 9 months ago.
43 stars 6.89 score 30 scripts
desctable
desctable:Produce Descriptive and Comparative Tables Easily
Easily create descriptive and comparative tables. It makes use and integrates directly with the tidyverse family of packages, and pipes. Tables are produced as (nested) dataframes for easy manipulation.
Maintained by Maxime Wack. Last updated 3 years ago.
52 stars 6.85 score 45 scriptsbioc
proActiv:Estimate Promoter Activity from RNA-Seq data
Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions.
Maintained by Joseph Lee. Last updated 5 months ago.
rnaseqgeneexpressiontranscriptionalternativesplicinggeneregulationdifferentialsplicingfunctionalgenomicsepigeneticstranscriptomicspreprocessingalternative-promotersgenomicspromoter-activitypromoter-annotationrna-seq-data
51 stars 6.66 score 15 scripts
mattheaphy
actxps:Create Actuarial Experience Studies: Prepare Data, Summarize Results, and Create Reports
Experience studies are used by actuaries to explore historical experience across blocks of business and to inform assumption setting activities. This package provides functions for preparing data, creating studies, visualizing results, and beginning assumption development. Experience study methods, including exposure calculations, are described in: Atkinson & McGarry (2016) "Experience Study Calculations" <https://www.soa.org/49378a/globalassets/assets/files/research/experience-study-calculations.pdf>. The limited fluctuation credibility method used by the 'exp_stats()' function is described in: Herzog (1999, ISBN:1-56698-374-6) "Introduction to Credibility Theory".
Maintained by Matt Heaphy. Last updated 3 months ago.
14 stars 6.38 score 23 scripts
hope-data-science
tidyft:Fast and Memory Efficient Data Operations in Tidy Syntax
Tidy syntax for 'data.table', using modification by reference whenever possible. This toolkit is designed for big data analysis in high-performance desktop or laptop computers. The syntax of the package is similar or identical to 'tidyverse'. It is user friendly, memory efficient and time saving. For more information, check its ancestor package 'tidyfst'.
Maintained by Tian-Yuan Huang. Last updated 6 months ago.
35 stars 6.25 score 34 scriptsbioc
plyxp:Data masks for SummarizedExperiment enabling dplyr-like manipulation
The package provides `rlang` data masks for the SummarizedExperiment class. The enables the evaluation of unquoted expression in different contexts of the SummarizedExperiment object with optional access to other contexts. The goal for `plyxp` is for evaluation to feel like a data.frame object without ever needing to unwind to a rectangular data.frame.
Maintained by Justin Landis. Last updated 12 days ago.
annotationgenomeannotationtranscriptomics
4 stars 5.88 score 6 scripts
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.
65 stars 5.81 score 8 scripts
ropensci
BaseSet:Working with Sets the Tidy Way
Implements a class and methods to work with sets, doing intersection, union, complementary sets, power sets, cartesian product and other set operations in a "tidy" way. These set operations are available for both classical sets and fuzzy sets. Import sets from several formats or from other several data structures.
Maintained by Lluís Revilla Sancho. Last updated 1 months ago.
bioconductorbioconductor-packagesets
11 stars 5.69 score 5 scripts
r-tidy-remote-sensing
tidyrgee:'tidyverse' Methods for 'Earth Engine'
Provides 'tidyverse' methods for wrangling and analyzing 'Earth Engine' <https://earthengine.google.com/> data. These methods help the user with filtering, joining and summarising 'Earth Engine' image collections.
Maintained by Zack Arno. Last updated 2 years ago.
48 stars 5.53 score 140 scripts
forestgeo
fgeo.tool:Import and Manipulate 'ForestGEO' Data
To help you access, transform, analyze, and visualize 'ForestGEO' data, we developed a collection of R packages (<https://forestgeo.github.io/fgeo/>). This package, in particular, helps you to easily import, filter, and modify 'ForestGEO' data. To learn more about 'ForestGEO' visit <https://forestgeo.si.edu/>.
Maintained by Mauro Lepore. Last updated 3 years ago.
dynamicsecologyfgeoforestgeomiscelaneastoolstreeutils
2 stars 4.86 score 27 scripts 3 dependents
korap
RKorAPClient:'KorAP' Web Service Client Package
A client package that makes the 'KorAP' web service API accessible from R. The corpus analysis platform 'KorAP' has been developed as a scientific tool to make potentially large, stratified and multiply annotated corpora, such as the 'German Reference Corpus DeReKo' or the 'Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify hypotheses and to find interesting patterns in real language use. The 'RKorAPClient' package provides access to 'KorAP' and the corpora behind it for user-created R code, as a programmatic alternative to the 'KorAP' web user-interface. You can learn more about 'KorAP' and use it directly on 'DeReKo' at <https://korap.ids-mannheim.de/>.
Maintained by Marc Kupietz. Last updated 28 days ago.
6 stars 4.81 score 30 scriptsbioc
plyinteractions:Extending tidy verbs to genomic interactions
Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.
Maintained by Jacques Serizay. Last updated 5 months ago.
4.75 score 14 scripts
poissonconsulting
mcmcdata:Manipulate MCMC Samples and Data Frames
Manipulates Monte Carlo Markov Chain samples and associated data frames.
Maintained by Joe Thorley. Last updated 2 months ago.
1 stars 3.56 score 4 scripts 4 dependents
r-forge
pems.utils:Portable Emissions (and Other Mobile) Measurement System Utilities
Utility functions for the handling, analysis and visualisation of data from portable emissions measurement systems ('PEMS') and other similar mobile activity monitoring devices. The package includes a dedicated 'pems' data class that manages many of the quality control, unit handling and data archiving issues that can hinder efforts to standardise 'PEMS' research.
Maintained by Karl Ropkins. Last updated 3 months ago.
3.06 score 19 scripts