R-universe search: arrange

randy3k

arrangements:Fast Generators and Iterators for Permutations, Combinations, Integer Partitions and Compositions

Fast generators and iterators for permutations, combinations, integer partitions and compositions. The arrangements are in lexicographical order and generated iteratively in a memory efficient manner. It has been demonstrated that 'arrangements' outperforms most existing packages of similar kind. Benchmarks could be found at <https://randy3k.github.io/arrangements/articles/benchmark.html>.

Maintained by Randy Lai. Last updated 2 years ago.

gmp

52.6 match 52 stars 7.89 score 118 scripts 23 dependents

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

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

didiermurillof

FielDHub:A Shiny App for Design of Experiments in Life Sciences

A shiny design of experiments (DOE) app that aids in the creation of traditional, un-replicated, augmented and partially-replicated designs applied to agriculture, plant breeding, forestry, animal and biological sciences.

Maintained by Didier Murillo. Last updated 8 months ago.

agricultural breeding design doe experimental plantbreeding shiny

10.7 match 48 stars 9.10 score 70 scripts 1 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.

5.8 match 1.2k stars 16.68 score 65k scripts 409 dependents

willgearty

deeptime:Plotting Tools for Anyone Working in Deep Time

Extends the functionality of other plotting packages (notably 'ggplot2') to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data. The primary goal of 'deeptime' is to enable users to add highly customizable timescales to their visualizations. Other functions are also included to assist with other areas of deep time visualization.

Maintained by William Gearty. Last updated 3 months ago.

geology ggplot2 paleontology visualization

7.7 match 92 stars 10.61 score 207 scripts 3 dependents

ludvigolsen

rearrr:Rearranging Data

Arrange data by a set of methods. Use rearrangers to reorder data points and mutators to change their values. From basic utilities, to centering the greatest value, to swirling in 3-dimensional space, 'rearrr' enables creativity when plotting and experimenting with data.

Maintained by Ludvig Renbo Olsen. Last updated 10 days ago.

arrange cluster expand forming generate ggplot2 order plotting-in-r roll rotate shaping swirl transformations

10.5 match 24 stars 7.26 score 128 scripts 8 dependents

wilkelab

cowplot:Streamlined Plot Theme and Plot Annotations for 'ggplot2'

Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.

Maintained by Claus O. Wilke. Last updated 2 months ago.

3.7 match 714 stars 18.83 score 75k scripts 1.4k dependents

yunuuuu

ggalign:A 'ggplot2' Extension for Consistent Axis Alignment

A 'ggplot2' extension offers various tools the creation of complex, multi-plot visualizations. Built on the familiar grammar of graphics, it provides intuitive tools to align and organize plots, making it ideal for complex visualizations. It excels in multi-omics research—such as genomics and microbiomes—by simplifying the visualization of intricate relationships between datasets, for example, linking genes to pathways. Whether you need to stack plots, arrange them around a central figure, or create a circular layout, 'ggalign' delivers flexibility and accuracy with minimal effort.

Maintained by Yun Peng. Last updated 1 days ago.

complex-heatmaps dendrogram dendrogram-heatmap ggplot ggplot-extension ggplot2 heatmap heatmap-visualization heatmaps marginal-plots oncoplot oncoprint tanglegram upset upsetplot

9.7 match 267 stars 7.08 score 27 scripts

eclarke

ggbeeswarm:Categorical Scatter (Violin Point) Plots

Provides two methods of plotting categorical scatter plots such that the arrangement of points within a category reflects the density of data at that region, and avoids over-plotting.

Maintained by Erik Clarke. Last updated 4 months ago.

4.0 match 550 stars 15.45 score 7.6k scripts 84 dependents

r-lib

gtable:Arrange 'Grobs' in Tables

Tools to make it easier to work with "tables" of 'grobs'. The 'gtable' package defines a 'gtable' grob class that specifies a grid along with a list of grobs and their placement in the grid. Further the package makes it easy to manipulate and combine 'gtable' objects so that complex compositions can be built up sequentially.

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

3.3 match 91 stars 18.09 score 4.1k scripts 7.6k 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.

d3js data-visualization ggplot2 javascript plotly shiny webgl

3.0 match 2.6k stars 19.43 score 93k scripts 797 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.

5.0 match 458 stars 11.41 score 732 scripts 10 dependents

mbedward

packcircles:Circle Packing

Algorithms to find arrangements of non-overlapping circles.

Maintained by Michael Bedward. Last updated 4 months ago.

cpp

5.7 match 57 stars 10.06 score 422 scripts 6 dependents

tidyverse

dtplyr:Data Table Back-End for 'dplyr'

Provides a data.table backend for 'dplyr'. The goal of 'dtplyr' is to allow you to write 'dplyr' code that is automatically translated to the equivalent, but usually much faster, data.table code.

Maintained by Hadley Wickham. Last updated 2 months ago.

datatable dplyr

3.4 match 671 stars 16.27 score 2.5k scripts 147 dependents

hadley

plyr:Tools for Splitting, Applying and Combining Data

A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. The development of 'plyr' has been generously supported by 'Becton Dickinson'.

Maintained by Hadley Wickham. Last updated 4 months ago.

cpp

3.0 match 500 stars 18.16 score 83k scripts 3.3k 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

5.0 match 341 stars 10.79 score 156 scripts 27 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.

annotation clustering genesetenrichment go kegg multiplecomparison pathways reactome visualization enrichment-analysis gsea

3.0 match 1.1k stars 17.03 score 11k scripts 48 dependents

cran

CVD:Color Vision Deficiencies

Methods for color vision deficiencies (CVD), to help understanding and mitigating issues with CVDs and to generate tests for diagnosis and interpretation.

Maintained by Jose Gama. Last updated 8 years ago.

27.1 match 1.78 score

bioc

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 5 months ago.

assaydomain infrastructure rnaseq differentialexpression geneexpression normalization clustering qualitycontrol sequencing transcription transcriptomics bioconductor bulk-transcriptional-analyses deseq2 differential-expression edger ensembl-ids entrez gene-symbols gsea mds-dimensions pca pipe redundancy tibble tidy tidy-data tidyverse transcripts tsne

4.9 match 168 stars 9.48 score 172 scripts 1 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

3.0 match 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 1 months ago.

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

3.0 match 553 stars 14.74 score 4.6k scripts 136 dependents

branchlab

metasnf:Meta Clustering with Similarity Network Fusion

Framework to facilitate patient subtyping with similarity network fusion and meta clustering. The similarity network fusion (SNF) algorithm was introduced by Wang et al. (2014) in <doi:10.1038/nmeth.2810>. SNF is a data integration approach that can transform high-dimensional and diverse data types into a single similarity network suitable for clustering with minimal loss of information from each initial data source. The meta clustering approach was introduced by Caruana et al. (2006) in <doi:10.1109/ICDM.2006.103>. Meta clustering involves generating a wide range of cluster solutions by adjusting clustering hyperparameters, then clustering the solutions themselves into a manageable number of qualitatively similar solutions, and finally characterizing representative solutions to find ones that are best for the user's specific context. This package provides a framework to easily transform multi-modal data into a wide range of similarity network fusion-derived cluster solutions as well as to visualize, characterize, and validate those solutions. Core package functionality includes easy customization of distance metrics, clustering algorithms, and SNF hyperparameters to generate diverse clustering solutions; calculation and plotting of associations between features, between patients, and between cluster solutions; and standard cluster validation approaches including resampled measures of cluster stability, standard metrics of cluster quality, and label propagation to evaluate generalizability in unseen data. Associated vignettes guide the user through using the package to identify patient subtypes while adhering to best practices for unsupervised learning.

Maintained by Prashanth S Velayudhan. Last updated 5 days ago.

bioinformatics clustering metaclustering snf

5.0 match 8 stars 8.21 score 30 scripts

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 1 days ago.

terra ggplot-extension r-spatial rspatial

3.0 match 191 stars 13.62 score 1.9k scripts 25 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

3.0 match 54 stars 13.25 score 584 scripts 128 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.

6.8 match 65 stars 5.81 score 8 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

3.0 match 143 stars 12.60 score 1.9k scripts 20 dependents

momx

Momocs:Morphometrics using R

The goal of 'Momocs' is to provide a complete, convenient, reproducible and open-source toolkit for 2D morphometrics. It includes most common 2D morphometrics approaches on outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout. It allows reproducible, complex morphometrics analyses and other morphometrics approaches should be easy to plug in, or develop from, on top of this canvas.

Maintained by Vincent Bonhomme. Last updated 1 years ago.

morphometrics

5.0 match 51 stars 7.42 score 346 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

1.9 match 481 stars 19.72 score 5.2k scripts 736 dependents

angabrio

missingHE:Missing Outcome Data in Health Economic Evaluation

Contains a suite of functions for health economic evaluations with missing outcome data. The package can fit different types of statistical models under a fully Bayesian approach using the software 'JAGS' (which should be installed locally and which is loaded in 'missingHE' via the 'R' package 'R2jags'). Three classes of models can be fitted under a variety of missing data assumptions: selection models, pattern mixture models and hurdle models. In addition to model fitting, 'missingHE' provides a set of specialised functions to assess model convergence and fit, and to summarise the statistical and economic results using different types of measures and graphs. The methods implemented are described in Mason (2018) <doi:10.1002/hec.3793>, Molenberghs (2000) <doi:10.1007/978-1-4419-0300-6_18> and Gabrio (2019) <doi:10.1002/sim.8045>.

Maintained by Andrea Gabrio. Last updated 2 years ago.

cost-effectiveness-analysis health-economic-evaluation individual-level-data jags missing-data parametric-modelling sensitivity-analysis cpp

6.8 match 5 stars 5.38 score 24 scripts

stan-dev

bayesplot:Plotting for Bayesian Models

Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow advocated in Gabry, Simpson, Vehtari, Betancourt, and Gelman (2019) <doi:10.1111/rssa.12378>. The package is designed not only to provide convenient functionality for users, but also a common set of functions that can be easily used by developers working on a variety of R packages for Bayesian modeling, particularly (but not exclusively) packages interfacing with 'Stan'.

Maintained by Jonah Gabry. Last updated 1 months ago.

bayesian ggplot2 mcmc pandoc stan statistical-graphics visualization

2.0 match 436 stars 16.69 score 6.5k scripts 98 dependents

david-barnett

microViz:Microbiome Data Analysis and Visualization

Microbiome data visualization and statistics tools built upon phyloseq.

Maintained by David Barnett. Last updated 3 months ago.

microbiome microbiome-analysis microbiota

5.3 match 114 stars 6.22 score 480 scripts

tokami

TropFishR:Tropical Fisheries Analysis

A compilation of fish stock assessment methods for the analysis of length-frequency data in the context of data-poor fisheries. Includes methods and examples included in the FAO Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish stock assessment" (<http://www.fao.org/documents/card/en/c/9bb12a06-2f05-5dcb-a6ca-2d6dd3080f65/>), as well as other more recent methods.

Maintained by Tobias K. Mildenberger. Last updated 5 months ago.

assessment fao-manual fish fish-stocks

4.0 match 25 stars 8.12 score 149 scripts

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.

3.2 match 98 stars 10.09 score 118 scripts 4 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 9 months ago.

cv ozunconf18 resume unconf

3.0 match 1.2k stars 10.78 score 556 scripts

dfsp-spirit

fsbrain:Managing and Visualizing Brain Surface Data

Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.

Maintained by Tim Schäfer. Last updated 4 months ago.

3d brain dti freesurfer mesh mri neuroimaging research surface visualization voxel

5.0 match 66 stars 6.47 score 15 scripts

martin3141

spant:MR Spectroscopy Analysis Tools

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.

Maintained by Martin Wilson. Last updated 1 months ago.

brain mri mrs mrshub spectroscopy fortran

3.8 match 25 stars 8.52 score 81 scripts

kassambara

survminer:Drawing Survival Curves using 'ggplot2'

Contains the function 'ggsurvplot()' for drawing easily beautiful and 'ready-to-publish' survival curves with the 'number at risk' table and 'censoring count plot'. Other functions are also available to plot adjusted curves for `Cox` model and to visually examine 'Cox' model assumptions.

Maintained by Alboukadel Kassambara. Last updated 5 months ago.

2.0 match 524 stars 15.87 score 7.0k scripts 55 dependents

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 4 months ago.

3.0 match 41 stars 10.54 score 418 scripts

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

3.5 match 48 stars 9.00 score 93 scripts 5 dependents

bioc

shiny.gosling:A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization for R and Shiny

A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. http://gosling-lang.org/. This R package is based on gosling.js. It uses R functions to create gosling plots that could be embedded onto R Shiny apps.

Maintained by Appsilon. Last updated 5 months ago.

shinyapps genetics visualization

5.1 match 6.08 score 53 scripts 1 dependents

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.

4.9 match 35 stars 6.25 score 34 scripts

r-tmap

tmap:Thematic Maps

Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.

Maintained by Martijn Tennekes. Last updated 5 days ago.

choropleth-maps maps spatial thematic-maps visualisation

1.8 match 880 stars 16.73 score 13k scripts 24 dependents

radiant-rstats

radiant.data:Data Menu for Radiant: Business Analytics using R and Shiny

The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.

Maintained by Vincent Nijs. Last updated 5 months ago.

3.6 match 54 stars 8.30 score 146 scripts 6 dependents

baptiste

egg:Extensions for 'ggplot2': Custom Geom, Custom Themes, Plot Alignment, Labelled Panels, Symmetric Scales, and Fixed Panel Size

Miscellaneous functions to help customise 'ggplot2' objects. High-level functions are provided to post-process 'ggplot2' layouts and allow alignment between plot panels, as well as setting panel sizes to fixed values. Other functions include a custom 'geom', and helper functions to enforce symmetric scales or add tags to facetted plots.

Maintained by Baptiste Auguie. Last updated 4 years ago.

2.5 match 13 stars 11.84 score 2.4k scripts 67 dependents

bzhanglab

WebGestaltR:Gene Set Analysis Toolkit WebGestaltR

The web version WebGestalt <https://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.

Maintained by John Elizarraras. Last updated 1 months ago.

rust cargo

3.2 match 35 stars 9.14 score 180 scripts

jokergoo

circlize:Circular Visualization

Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data. The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.

Maintained by Zuguang Gu. Last updated 1 years ago.

1.9 match 983 stars 15.62 score 10k scripts 213 dependents

bioc

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.

visualization microbiome software multiplecomparison featureextraction microbiome-analysis microbiome-data

3.0 match 183 stars 9.70 score 126 scripts 1 dependents

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 26 days ago.

bioconductor bioconductor-package sets

5.0 match 11 stars 5.69 score 5 scripts

kassambara

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.

1.9 match 456 stars 15.16 score 11k scripts 420 dependents

cran

ggtern:An Extension to 'ggplot2', for the Creation of Ternary Diagrams

Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website.

Maintained by Nicholas Hamilton. Last updated 12 months ago.

4.0 match 4 stars 7.05 score 1.1k scripts 6 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

1.9 match 222 stars 14.71 score 436 scripts 119 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 1 months ago.

3.0 match 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.

3.0 match 55 stars 9.07 score 389 scripts 11 dependents

uligges

klaR:Classification and Visualization

Miscellaneous functions for classification and visualization, e.g. regularized discriminant analysis, sknn() kernel-density naive Bayes, an interface to 'svmlight' and stepclass() wrapper variable selection for supervised classification, partimat() visualization of classification rules and shardsplot() of cluster results as well as kmodes() clustering for categorical data, corclust() variable clustering, variable extraction from different variable clustering models and weight of evidence preprocessing.

Maintained by Uwe Ligges. Last updated 1 years ago.

3.5 match 5 stars 7.61 score 1.4k scripts 13 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, competing risks and recurrent events data. 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 2 months ago.

additive-models pamm pammtools piece-wise-exponential survival-analysis

3.0 match 48 stars 8.78 score 310 scripts 8 dependents

indrajeetpatil

ggstatsplot:'ggplot2' Based Plots with Statistical Details

Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests included in the plots themselves. It provides an easier syntax to generate information-rich plots for statistical analysis of continuous (violin plots, scatterplots, histograms, dot plots, dot-and-whisker plots) or categorical (pie and bar charts) data. Currently, it supports the most common types of statistical approaches and tests: parametric, nonparametric, robust, and Bayesian versions of t-test/ANOVA, correlation analyses, contingency table analysis, meta-analysis, and regression analyses. References: Patil (2021) <doi:10.21105/joss.03236>.

Maintained by Indrajeet Patil. Last updated 20 days ago.

bayes-factors datascience dataviz effect-size ggplot-extension hypothesis-testing non-parametric-statistics regression-models statistical-analysis

1.8 match 2.1k stars 14.49 score 3.0k scripts 1 dependents

radicalcommecol

cxr:A Toolbox for Modelling Species Coexistence in R

Recent developments in modern coexistence theory have advanced our understanding on how species are able to persist and co-occur with other species at varying abundances. However, applying this mathematical framework to empirical data is still challenging, precluding a larger adoption of the theoretical tools developed by empiricists. This package provides a complete toolbox for modelling interaction effects between species, and calculate fitness and niche differences. The functions are flexible, may accept covariates, and different fitting algorithms can be used. A full description of the underlying methods is available in García-Callejas, D., Godoy, O., and Bartomeus, I. (2020) <doi:10.1111/2041-210X.13443>. Furthermore, the package provides a series of functions to calculate dynamics for stage-structured populations across sites.

Maintained by David Garcia-Callejas. Last updated 1 months ago.

4.0 match 10 stars 6.51 score 27 scripts

rstudio

crosstalk:Inter-Widget Interactivity for HTML Widgets

Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). Currently supports linked brushing and filtering.

Maintained by Carson Sievert. Last updated 2 months ago.

1.8 match 292 stars 14.69 score 1.6k scripts 1.5k dependents

insightsengineering

tern:Create Common TLGs Used in Clinical Trials

Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials.

Maintained by Joe Zhu. Last updated 2 months ago.

clinical-trials graphs listings nest outputs tables

2.0 match 79 stars 12.62 score 186 scripts 9 dependents

skranz

dplyrExtras:extra functionality for dplyr like mutate_rows for mutation of a subset of rows

Some extra functionality that is not (yet) in dplyr, e.g. mutate_rows (mutation of subset of rows) xsummarise_each (summarise_each with more flexible alignment of results), or s_filter, s_arrange ,... that allow string arguments.

Maintained by Sebastian Kranz. Last updated 5 years ago.

dplyr

5.1 match 20 stars 4.85 score 59 scripts 4 dependents

tidymodels

corrr:Correlations in R

A tool for exploring correlations. It makes it possible to easily perform routine tasks when exploring correlation matrices such as ignoring the diagonal, focusing on the correlations of certain variables against others, or rearranging and visualizing the matrix in terms of the strength of the correlations.

Maintained by Max Kuhn. Last updated 1 years ago.

1.8 match 593 stars 13.82 score 2.9k scripts 7 dependents

bradyajohnston

figpatch:Easily Arrange External Figures with Patchwork Alongside 'ggplot2' Figures

For including external figures into an assembled {patchwork}. This enables the creation of more complex figures that include images alongside plots.

Maintained by Brady Johnston. Last updated 2 months ago.

alignment ggplot2 patchwork rmarkdown

4.6 match 77 stars 5.37 score 61 scripts

bioc

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.

software infrastructure

5.0 match 4.75 score 14 scripts

jbkunst

highcharter:A Wrapper for the 'Highcharts' Library

A wrapper for the 'Highcharts' library including shortcut functions to plot R objects. 'Highcharts' <https://www.highcharts.com/> is a charting library offering numerous chart types with a simple configuration syntax.

Maintained by Joshua Kunst. Last updated 1 years ago.

highcharts htmlwidgets shiny shiny-r visualization wrapper

1.7 match 725 stars 13.93 score 4.9k scripts 18 dependents

bioc

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 5 months ago.

annotation genomeannotation transcriptomics

4.9 match 4 stars 4.81 score 6 scripts

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 1 months ago.

adat proteomics proteomics-data-analysis somascan

3.0 match 26 stars 7.71 score 132 scripts

molgenis

dsTidyverseClient:'DataSHIELD' 'Tidyverse' Clientside Package

Implementation of selected 'Tidyverse' functions within 'DataSHIELD', an open-source federated analysis solution in R. Currently, 'DataSHIELD' contains very limited tools for data manipulation, so the aim of this package is to improve the researcher experience by implementing essential functions for data manipulation, including subsetting, filtering, grouping, and renaming variables. This is the clientside package which should be installed locally, and is used in conjuncture with the serverside package 'dsTidyverse' which is installed on the remote server holding the data. For more information, see <https://www.tidyverse.org/>, <https://datashield.org/> and <https://github.com/molgenis/ds-tidyverse>.

Maintained by Tim Cadman. Last updated 18 days ago.

4.3 match 1 stars 5.43 score 2 scripts

bioc

ggbio:Visualization tools for genomic data

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

Maintained by Michael Lawrence. Last updated 5 months ago.

infrastructure visualization

1.9 match 111 stars 12.26 score 734 scripts 17 dependents

spatstat

spatstat.geom:Geometrical Functionality of the 'spatstat' Family

Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)

Maintained by Adrian Baddeley. Last updated 2 days ago.

classes-and-objects distance-calculation geometry geometry-processing images mensuration plotting point-patterns spatial-data spatial-data-analysis

1.8 match 7 stars 12.11 score 241 scripts 227 dependents

hafen

geofacet:'ggplot2' Faceting Utilities for Geographical Data

Provides geographical faceting functionality for 'ggplot2'. Geographical faceting arranges a sequence of plots of data for different geographical entities into a grid that preserves some of the geographical orientation.

Maintained by Ryan Hafen. Last updated 7 months ago.

geography ggplot2 visualization

2.2 match 340 stars 9.78 score 1.5k scripts 4 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 8 months ago.

3.0 match 43 stars 6.89 score 30 scripts

ycroissant

dfidx:Indexed Data Frames

Provides extended data frames, with a special data frame column which contains two indexes, with potentially a nesting structure.

Maintained by Yves Croissant. Last updated 7 months ago.

3.0 match 2 stars 6.85 score 44 scripts 18 dependents

bioc

ggcyto:Visualize Cytometry data with ggplot

With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.

Maintained by Mike Jiang. Last updated 5 months ago.

immunooncology flowcytometry cellbasedassays infrastructure visualization

1.8 match 58 stars 11.25 score 362 scripts 5 dependents

jthomasmock

gtExtras:Extending 'gt' for Beautiful HTML Tables

Provides additional functions for creating beautiful tables with 'gt'. The functions are generally wrappers around boilerplate or adding opinionated niche capabilities and helpers functions.

Maintained by Thomas Mock. Last updated 12 months ago.

data-science data-visualization datascience ggplot2 gt plots sparkline sparkline-graphs sparklines tables

1.8 match 199 stars 11.45 score 2.4k scripts 3 dependents

famuvie

breedR:Statistical Methods for Forest Genetic Resources Analysts

Statistical tools to build predictive models for the breeders community. It aims to assess the genetic value of individuals under a number of situations, including spatial autocorrelation, genetic/environment interaction and competition. It is under active development as part of the Trees4Future project, particularly developed having forest genetic trials in mind. But can be used for animals or other situations as well.

Maintained by Facundo Muñoz. Last updated 8 months ago.

3.7 match 33 stars 5.44 score 24 scripts

bioc

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.

rnaseq geneexpression transcription alternativesplicing generegulation differentialsplicing functionalgenomics epigenetics transcriptomics preprocessing alternative-promoters genomics promoter-activity promoter-annotation rna-seq-data

3.0 match 51 stars 6.66 score 15 scripts

dmurdoch

plotrix:Various Plotting Functions

Lots of plots, various labeling, axis and color scaling functions. The author/maintainer died in September 2023.

Maintained by Duncan Murdoch. Last updated 1 years ago.

1.8 match 5 stars 11.31 score 9.2k scripts 361 dependents

myles-lewis

locuszoomr:Gene Locus Plot with Gene Annotations

Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.

Maintained by Myles Lewis. Last updated 14 days ago.

2.6 match 40 stars 7.43 score 50 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 2 months ago.

3.0 match 14 stars 6.38 score 23 scripts

gtatters

Thermimage:Thermal Image Analysis

A collection of functions and routines for inputting thermal image video files, plotting and converting binary raw data into estimates of temperature. First published 2015-03-26. Written primarily for research purposes in biological applications of thermal images. v1 included the base calculations for converting thermal image binary values to temperatures. v2 included additional equations for providing heat transfer calculations and an import function for thermal image files (v2.2.3 fixed error importing thermal image to windows OS). v3. Added numerous functions for converting thermal image, videos, rewriting and exporting. v3.1. Added new functions to convert files. v3.2. Fixed the various functions related to finding frame times. v4.0. fixed an error in atmospheric attenuation constants, affecting raw2temp and temp2raw functions. Recommend update for use with long distance calculations. v.4.1.3. changed to frameLocates to reflect change to as.character() to format().

Maintained by Glenn J. Tattersall. Last updated 3 years ago.

animal-physiology heat-exchange heat-flux image-frames temperature thermal-biology thermal-images

3.3 match 169 stars 5.85 score 83 scripts

ropensci

refsplitr:author name disambiguation, author georeferencing, and mapping of coauthorship networks with 'Web of Science' data

Tools to parse and organize reference records downloaded from the 'Web of Science' citation database into an R-friendly format, disambiguate the names of authors, geocode their locations, and generate/visualize coauthorship networks. This package has been peer-reviewed by rOpenSci (v. 1.0).

Maintained by Emilio Bruna. Last updated 7 months ago.

name disambiguation bibliometrics coauthorship collaboration georeferencing metascience references scientometrics science of science web of science

3.3 match 55 stars 5.64 score 16 scripts

tomasfryda

h2o:R Interface for the 'H2O' Scalable Machine Learning Platform

R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection, Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).

Maintained by Tomas Fryda. Last updated 1 years ago.

2.3 match 3 stars 8.20 score 7.8k scripts 11 dependents

jl5000

tidyged.utils:Utilities to Manage GEDCOM Files Using Tidyverse Principles

Various utilities to manage and clean family tree GEDCOM files using tidy dataframes.

Maintained by Jamie Lendrum. Last updated 3 years ago.

4.6 match 3.88 score 6 scripts 1 dependents

krassowski

ComplexUpset:Create Complex UpSet Plots Using 'ggplot2' Components

UpSet plots are an improvement over Venn Diagram for set overlap visualizations. Striving to bring the best of the 'UpSetR' and 'ggplot2', this package offers a way to create complex overlap visualisations, using simple and familiar tools, i.e. geoms of 'ggplot2'. For introduction to UpSet concept, see Lex et al. (2014) <doi:10.1109/TVCG.2014.2346248>.

Maintained by Michał Krassowski. Last updated 1 years ago.

ggplot ggplot2 patchwork python rstat upset upsetr venn venn-diagram visualization

1.9 match 491 stars 9.54 score 554 scripts 4 dependents

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.

5.0 match 1 stars 3.56 score 4 scripts 4 dependents

nepem-ufsc

metan:Multi Environment Trials Analysis

Performs stability analysis of multi-environment trial data using parametric and non-parametric methods. Parametric methods includes Additive Main Effects and Multiplicative Interaction (AMMI) analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>, Ecovalence by Wricke (1965), Genotype plus Genotype-Environment (GGE) biplot analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>, geometric adaptability index by Mohammadi & Amri (2008) <doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart & Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>, genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's (2004) method, power law residuals (POLAR) statistics by Doring et al. (2015) <doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>, stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>, weighted average of absolute scores by Olivoto et al. (2019a) <doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>. Non-parametric methods includes superiority index by Lin & Binns (1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic stability by Huehn (1990) <doi:10.1007/BF00024241>, TOP third statistic by Fox et al. (1990) <doi:10.1007/BF00040364>. Functions for computing biometrical analysis such as path analysis, canonical correlation, partial correlation, clustering analysis, and tools for inspecting, manipulating, summarizing and plotting typical multi-environment trial data are also provided.

Maintained by Tiago Olivoto. Last updated 10 days ago.

1.9 match 2 stars 9.48 score 1.3k scripts 2 dependents

r-lib

gargle:Utilities for Working with Google APIs

Provides utilities for working with Google APIs <https://developers.google.com/apis-explorer>. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.

Maintained by Jennifer Bryan. Last updated 2 years ago.

authentication google

1.2 match 113 stars 14.88 score 266 scripts 192 dependents

dardisco

survMisc:Miscellaneous Functions for Survival Data

A collection of functions to help in the analysis of right-censored survival data. These extend the methods available in package:survival.

Maintained by Chris Dardis. Last updated 5 years ago.

1.8 match 1 stars 9.49 score 218 scripts 55 dependents

brry

berryFunctions:Function Collection Related to Plotting and Hydrology

Draw horizontal histograms, color scattered points by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, trace errors and warnings, use the unit hydrograph in a linear storage cascade, convert lists to data.frames and arrays, fit multiple functions.

Maintained by Berry Boessenkool. Last updated 1 months ago.

1.8 match 13 stars 9.43 score 350 scripts 16 dependents

ncss-tech

sharpshootR:A Soil Survey Toolkit

A collection of data processing, visualization, and export functions to support soil survey operations. Many of the functions build on the `SoilProfileCollection` S4 class provided by the aqp package, extending baseline visualization to more elaborate depictions in the context of spatial and taxonomic data. While this package is primarily developed by and for the USDA-NRCS, in support of the National Cooperative Soil Survey, the authors strive for generalization sufficient to support any soil survey operation. Many of the included functions are used by the SoilWeb suite of websites and movile applications. These functions are provided here, with additional documentation, to enable others to replicate high quality versions of these figures for their own purposes.

Maintained by Dylan Beaudette. Last updated 13 days ago.

1.9 match 18 stars 8.37 score 327 scripts

bioc

muscat:Multi-sample multi-group scRNA-seq data analysis tools

`muscat` provides various methods and visualization tools for DS analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated “pseudobulk” data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.

Maintained by Helena L. Crowell. Last updated 5 months ago.

immunooncology differentialexpression sequencing singlecell software statisticalmethod visualization

1.5 match 181 stars 10.26 score 686 scripts

kcuilla

reactablefmtr:Streamlined Table Styling and Formatting for Reactable

Provides various features to streamline and enhance the styling of interactive reactable tables with easy-to-use and highly-customizable functions and themes. Apply conditional formatting to cells with data bars, color scales, color tiles, and icon sets. Utilize custom table themes inspired by popular websites such and bootstrap themes. Apply sparkline line & bar charts (note this feature requires the 'dataui' package which can be downloaded from <https://github.com/timelyportfolio/dataui>). Increase the portability and reproducibility of reactable tables by embedding images from the web directly into cells. Save the final table output as a static image or interactive file.

Maintained by Kyle Cuilla. Last updated 2 years ago.

customization data-visualization easy-to-use reproducible tables

1.8 match 209 stars 8.79 score 460 scripts 4 dependents

r-forge

modEvA:Model Evaluation and Analysis

Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.

Maintained by A. Marcia Barbosa. Last updated 11 days ago.

2.3 match 6.82 score 269 scripts 3 dependents

iohprofiler

IOHanalyzer:Data Analysis Part of 'IOHprofiler'

The data analysis module for the Iterative Optimization Heuristics Profiler ('IOHprofiler'). This module provides statistical analysis methods for the benchmark data generated by optimization heuristics, which can be visualized through a web-based interface. The benchmark data is usually generated by the experimentation module, called 'IOHexperimenter'. 'IOHanalyzer' also supports the widely used 'COCO' (Comparing Continuous Optimisers) data format for benchmarking.

Maintained by Diederick Vermetten. Last updated 10 months ago.

cpp

3.0 match 24 stars 5.10 score 13 scripts

stefanedwards

lemon:Freshing Up your 'ggplot2' Plots

Functions for working with legends and axis lines of 'ggplot2', facets that repeat axis lines on all panels, and some 'knitr' extensions.

Maintained by Stefan McKinnon Edwards. Last updated 4 months ago.

axis-lines facets ggplot-extension ggplot2 knitr legend ticks visualization

1.3 match 190 stars 11.98 score 1.7k scripts 4 dependents

cardiomoon

ztable:Zebra-Striped Tables in LaTeX and HTML Formats

Makes zebra-striped tables (tables with alternating row colors) in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova, glm, coxph, nls, fitdistr, mytable and cbind.mytable objects.

Maintained by Keon-Woong Moon. Last updated 2 years ago.

1.9 match 21 stars 7.90 score 212 scripts 2 dependents

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.

dynamics ecology fgeo forestgeo miscelaneas tools tree utils

3.0 match 2 stars 4.86 score 27 scripts 3 dependents

snoweye

pbdMPI:R Interface to MPI for HPC Clusters (Programming with Big Data Project)

A simplified, efficient, interface to MPI for HPC clusters. It is a derivation and rethinking of the Rmpi package. pbdMPI embraces the prevalent parallel programming style on HPC clusters. Beyond the interface, a collection of functions for global work with distributed data and resource-independent RNG reproducibility is included. It is based on S4 classes and methods.

Maintained by Wei-Chen Chen. Last updated 6 months ago.

openmpi

2.0 match 2 stars 7.11 score 179 scripts 3 dependents

dipterix

dipsaus:A Dipping Sauce for Data Analysis and Visualizations

Works as an "add-on" to packages like 'shiny', 'future', as well as 'rlang', and provides utility functions. Just like dipping sauce adding flavors to potato chips or pita bread, 'dipsaus' for data analysis and visualizations adds handy functions and enhancements to popular packages. The goal is to provide simple solutions that are frequently asked for online, such as how to synchronize 'shiny' inputs without freezing the app, or how to get memory size on 'Linux' or 'MacOS' system. The enhancements roughly fall into these four categories: 1. 'shiny' input widgets; 2. high-performance computing using the 'future' package; 3. modify R calls and convert among numbers, strings, and other objects. 4. utility functions to get system information such like CPU chip-set, memory limit, etc.

Maintained by Zhengjia Wang. Last updated 6 days ago.

cpp

1.8 match 13 stars 7.90 score 85 scripts 3 dependents

molgenis

dsTidyverse:'DataSHIELD' 'Tidyverse' Serverside Package

Implementation of selected 'Tidyverse' functions within 'DataSHIELD', an open-source federated analysis solution in R. Currently, DataSHIELD contains very limited tools for data manipulation, so the aim of this package is to improve the researcher experience by implementing essential functions for data manipulation, including subsetting, filtering, grouping, and renaming variables. This is the serverside package which should be installed on the server holding the data, and is used in conjuncture with the clientside package 'dsTidyverseClient' which is installed in the local R environment of the analyst. For more information, see <https://www.tidyverse.org/> and <https://datashield.org/>.

Maintained by Tim Cadman. Last updated 18 days ago.

3.0 match 2 stars 4.56 score 2 scripts

predictiveecology

quickPlot:A System of Plotting Optimized for Speed and Modularity

A high-level plotting system, compatible with `ggplot2` objects, maps from `sf`, `terra`, `raster`, `sp`. It is built primarily on the 'grid' package. The objective of the package is to provide a plotting system that is built for speed and modularity. This is useful for quick visualizations when testing code and for plotting multiple figures to the same device from independent sources that may be independent of one another (i.e., different function or modules the create the visualizations). The suggested package 'fastshp' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).

Maintained by Eliot J B McIntire. Last updated 4 months ago.

plotting visualization

1.7 match 6 stars 7.92 score 121 scripts 12 dependents

drg-123

NSM3:Functions and Datasets to Accompany Hollander, Wolfe, and Chicken - Nonparametric Statistical Methods, Third Edition

Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.

Maintained by Grant Schneider. Last updated 4 months ago.

3.6 match 1 stars 3.77 score 115 scripts 1 dependents

yikeshu0611

cutoff:Seek the Significant Cutoff Value

Seek the significant cutoff value for a continuous variable, which will be transformed into a classification, for linear regression, logistic regression, logrank analysis and cox regression. First of all, all combinations will be gotten by combn() function. Then n.per argument, abbreviated of total number percentage, will be used to remove the combination of smaller data group. In logistic, Cox regression and logrank analysis, we will also use p.per argument, patient percentage, to filter the lower proportion of patients in each group. Finally, p value in regression results will be used to get the significant combinations and output relevant parameters. In this package, there is no limit to the number of cutoff points, which can be 1, 2, 3 or more. Missing values will be deleted by na.omit() function before analysis.

Maintained by Jing Zhang. Last updated 5 years ago.

3.6 match 1 stars 3.67 score 31 scripts 1 dependents

epiverse-trace

linelist:Tagging and Validating Epidemiological Data

Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.

Maintained by Hugo Gruson. Last updated 23 days ago.

data data-structures epidemiology epiverse outbreaks sdg-3 structured-data

1.5 match 8 stars 8.80 score 61 scripts 2 dependents

rmi-pacta

r2dii.match:Tools to Match Corporate Lending Portfolios with Climate Data

These tools implement in R a fundamental part of the software 'PACTA' (Paris Agreement Capital Transition Assessment), which is a free tool that calculates the alignment between financial portfolios and climate scenarios (<https://www.transitionmonitor.com/>). Financial institutions use 'PACTA' to study how their capital allocation decisions align with climate change mitigation goals. This package matches data from corporate lending portfolios to asset level data from market-intelligence databases (e.g. power plant capacities, emission factors, etc.). This is the first step to assess if a financial portfolio aligns with climate goals.

Maintained by Jacob Kastl. Last updated 28 days ago.

climate-change

1.7 match 7 stars 7.63 score 118 scripts 2 dependents

kwb-r

kwb.plot:some useful functions for plotting

Some useful functions for plotting.

Maintained by Hauke Sonnenberg. Last updated 1 years ago.

data-visualisation project-fakin project-miacso

3.6 match 3.59 score 1 scripts 26 dependents

lcef97

SchoolDataIT:Retrieve, Harmonise and Map Open Data Regarding the Italian School System

Compiles and displays the available data sets regarding the Italian school system, with a focus on the infrastructural aspects. Input datasets are downloaded from the web, with the aim of updating everything to real time. The functions are divided in four main modules, namely 'Get', to scrape raw data from the web 'Util', various utilities needed to process raw data 'Group', to aggregate data at the municipality or province level 'Map', to visualize the output datasets.

Maintained by Leonardo Cefalo. Last updated 2 months ago.

3.3 match 3.88 score

cran

welchADF:Welch-James Statistic for Robust Hypothesis Testing under Heterocedasticity and Non-Normality

Implementation of Johansen's general formulation of Welch-James's statistic with Approximate Degrees of Freedom, which makes it suitable for testing any linear hypothesis concerning cell means in univariate and multivariate mixed model designs when the data pose non-normality and non-homogeneous variance. Some improvements, namely trimmed means and Winsorized variances, and bootstrapping for calculating an empirical critical value, have been added to the classical formulation. The code departs from a previous SAS implementation by L.M. Lix and H.J. Keselman, available at <http://supp.apa.org/psycarticles/supplemental/met_13_2_110/SAS_Program.pdf> and published in Keselman, H.J., Wilcox, R.R., and Lix, L.M. (2003) <DOI:10.1111/1469-8986.00060>.

Maintained by Pablo J. Villacorta. Last updated 6 years ago.

6.4 match 2.00 score

kjhealy

socviz:Utility Functions and Data Sets for Data Visualization

Supporting materials for a course and book on data visualization. It contains utility functions for graphs and several sample data sets. See Healy (2019) <ISBN 978-0691181622>.

Maintained by Kieran Healy. Last updated 5 years ago.

1.8 match 190 stars 7.09 score 628 scripts

koalaverse

sure:Surrogate Residuals for Ordinal and General Regression Models

An implementation of the surrogate approach to residuals and diagnostics for ordinal and general regression models; for details, see Liu and Zhang (2017, <doi:https://doi.org/10.1080/01621459.2017.1292915>) and Greenwell et al. (2017, <https://journal.r-project.org/archive/2018/RJ-2018-004/index.html>). These residuals can be used to construct standard residual plots for model diagnostics (e.g., residual-vs-fitted value plots, residual-vs-covariate plots, Q-Q plots, etc.). The package also provides an 'autoplot' function for producing standard diagnostic plots using 'ggplot2' graphics. The package currently supports cumulative link models from packages 'MASS', 'ordinal', 'rms', and 'VGAM'. Support for binary regression models using the standard 'glm' function is also available.

Maintained by Brandon Greenwell. Last updated 14 days ago.

categorical-data diagnostics ordinal-regression residuals

2.3 match 9 stars 5.58 score 47 scripts 1 dependents

hneth

ds4psy:Data Science for Psychologists

All datasets and functions required for the examples and exercises of the book "Data Science for Psychologists" (by Hansjoerg Neth, Konstanz University, 2023), freely available at <https://bookdown.org/hneth/ds4psy/>. The book and course introduce principles and methods of data science to students of psychology and other biological or social sciences. The 'ds4psy' package primarily provides datasets, but also functions for data generation and manipulation (e.g., of text and time data) and graphics that are used in the book and its exercises. All functions included in 'ds4psy' are designed to be explicit and instructive, rather than efficient or elegant.

Maintained by Hansjoerg Neth. Last updated 1 months ago.

data-literacy data-science education exploratory-data-analysis psychology social-sciences visualisation

1.8 match 22 stars 6.79 score 70 scripts

rstudio

connectwidgets:Organize and Curate Your Content Within 'Posit Connect'

A collection of helper functions and 'htmlwidgets' to help publishers curate content collections on 'Posit Connect'. The components, Card, Grid, Table, Search, and Filter can be used to produce a showcase page or gallery contained within a static or interactive R Markdown page.

Maintained by Brian Smith. Last updated 6 months ago.

1.8 match 22 stars 6.80 score 36 scripts

mirzaghaderi

rtpcr:qPCR Data Analysis

Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor), analysis of variance (ANOVA), analysis of covariance (ANCOVA) or analysis of repeated measure data to calculate the fold change (FC, Delta Delta Ct method) or relative expression (RE, Delta Ct method). The functions further provide standard errors and confidence intervals for means, apply statistical mean comparisons and present significance. To facilitate function application, different data sets were used as examples and the outputs were explained. ‘rtpcr’ package also provides bar plots using various controlling arguments. The 'rtpcr' package is user-friendly and easy to work with and provides an applicable resource for analyzing real-time PCR data.

Maintained by Ghader Mirzaghaderi. Last updated 26 days ago.

data-analysis qpcr

2.4 match 1 stars 4.88 score 3 scripts

vinhdizzo

IRexamples:Collection of Practical Institutional Research Examples and Tutorials

Provides examples of code for analyzing data or accomplishing tasks that may be useful to institutional or educational researchers.

Maintained by Vinh Nguyen. Last updated 2 years ago.

2.3 match 4 stars 5.00 score 4 scripts

nicchr

fastplyr:Fast Alternatives to 'tidyverse' Functions

A full set of fast data manipulation tools with a tidy front-end and a fast back-end using 'collapse' and 'cheapr'.

Maintained by Nick Christofides. Last updated 24 days ago.

cpp

1.8 match 23 stars 6.32 score 36 scripts 1 dependents

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.

1.7 match 120 stars 6.56 score 1 dependents

rafapereirabr

geobr:Download Official Spatial Data Sets of Brazil

Easy access to official spatial data sets of Brazil as 'sf' objects in R. The package includes a wide range of geospatial data available at various geographic scales and for various years with harmonized attributes, projection and fixed topology.

Maintained by Rafael H. M. Pereira. Last updated 6 months ago.

1.9 match 5.89 score 1.4k scripts 1 dependents

bioc

SingleMoleculeFootprinting:Analysis tools for Single Molecule Footprinting (SMF) data

SingleMoleculeFootprinting provides functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location.

Maintained by Guido Barzaghi. Last updated 28 days ago.

dnamethylation coverage nucleosomepositioning datarepresentation epigenetics methylseq qualitycontrol sequencing

1.7 match 2 stars 6.43 score 27 scripts

cran

Fragman:Fragment Analysis in R

Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).

Maintained by Giovanny Covarrubias-Pazaran. Last updated 7 years ago.

3.9 match 5 stars 2.65 score 1 dependents

bioc

CrispRVariants:Tools for counting and visualising mutations in a target location

CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.

Maintained by Helen Lindsay. Last updated 5 months ago.

immunooncology crispr genomicvariation variantdetection geneticvariability datarepresentation visualization sequencing

1.9 match 5.51 score 32 scripts

ruthckb

bubbleHeatmap:Produces 'bubbleHeatmap' Plots for Visualising Metabolomics Data

Plotting package based on the grid system, combining elements of a bubble plot and heatmap to conveniently display two numerical variables, (represented by color and size) grouped by categorical variables on the x and y axes. This is a useful alternative to a forest plot when the data can be grouped in two dimensions, such as predictors x outcomes. It has particular advantages for visualising the metabolic measures produced by the 'Nightingale Health' metabolomics platform, and templates are included for automatically generating figures from these datasets.

Maintained by Ruth Boxall. Last updated 2 years ago.

5.1 match 1 stars 2.00 score 3 scripts

bergsmat

metaplot:Data-Driven Plot Design

Designs plots in terms of core structure. See 'example(metaplot)'. Primary arguments are (unquoted) column names; order and type (numeric or not) dictate the resulting plot. Specify any y variables, x variable, any groups variable, and any conditioning variables to metaplot() to generate density plots, boxplots, mosaic plots, scatterplots, scatterplot matrices, or conditioned plots. Use multiplot() to arrange plots in grids. Wherever present, scalar column attributes 'label' and 'guide' are honored, producing fully annotated plots with minimal effort. Attribute 'guide' is typically units, but may be encoded() to provide interpretations of categorical values (see '?encode'). Utility unpack() transforms scalar column attributes to row values and pack() does the reverse, supporting tool-neutral storage of metadata along with primary data. The package supports customizable aesthetics such as such as reference lines, unity lines, smooths, log transformation, and linear fits. The user may choose between trellis and ggplot output. Compact syntax and integrated metadata promote workflow scalability.

Maintained by Tim Bergsma. Last updated 1 years ago.

2.3 match 2 stars 4.49 score 52 scripts 1 dependents

sjentsch

jmvReadWrite:Read and Write 'jamovi' Files ('.omv')

The free and open a statistical spreadsheet 'jamovi' (<https://www.jamovi.org>) aims to make statistical analyses easy and intuitive. 'jamovi' produces syntax that can directly be used in R (in connection with the R-package 'jmv'). Having import / export routines for the data files 'jamovi' produces ('.omv') permits an easy transfer of data and analyses between 'jamovi' and R.

Maintained by Sebastian Jentschke. Last updated 1 days ago.

jamovi

1.6 match 5 stars 6.09 score 32 scripts

npm27

lrd:A Package for Processing Lexical Response Data

Lexical response data is a package that can be used for processing cued-recall, free-recall, and sentence responses from memory experiments.

Maintained by Nicholas Maxwell. Last updated 3 years ago.

1.8 match 3 stars 5.30 score 33 scripts

dkibalnikov

donutsk:Construct Advanced Donut Charts

Build donut/pie charts with 'ggplot2' layer by layer, exploiting the advantages of polar symmetry. Leverage layouts to distribute labels effectively. Connect labels to donut segments using pins. Streamline annotation and highlighting.

Maintained by Dmitry Kibalnikov. Last updated 11 months ago.

1.8 match 6 stars 5.18 score 2 scripts

henningte

ir:Functions to Handle and Preprocess Infrared Spectra

Functions to import and handle infrared spectra (import from '.csv' and Thermo Galactic's '.spc', baseline correction, binning, clipping, interpolating, smoothing, averaging, adding, subtracting, dividing, multiplying, plotting).

Maintained by Henning Teickner. Last updated 3 years ago.

chemometrics infrared infrared-spectra ir-package mid-infrared-spectra spectroscopy

1.8 match 6 stars 5.32 score 35 scripts

bioc

sigFeature:sigFeature: Significant feature selection using SVM-RFE & t-statistic

This package provides a novel feature selection algorithm for binary classification using support vector machine recursive feature elimination SVM-RFE and t-statistic. In this feature selection process, the selected features are differentially significant between the two classes and also they are good classifier with higher degree of classification accuracy.

Maintained by Pijush Das Developer. Last updated 5 months ago.

featureextraction geneexpression microarray transcription mrnamicroarray geneprediction normalization classification supportvectormachine

1.9 match 4.92 score 21 scripts

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 2 months ago.

openjdk

3.0 match 3.06 score 19 scripts

oli-heller

SoilManageR:Calculate Soil Management Indicators for Agricultural Practice Assessment

Calculate numerical agricultural soil management indicators from on a management timeline of an arable field. Currently, indicators for carbon (C) input into the soil system, soil tillage intensity rating (STIR), number of soil cover and living plant cover days, N fertilization and livestock intensity, and plant diversity are implemented. The functions can also be used independently of the management timeline to calculate some indicators. The package contains tables with reference information for the functions, as well as a '*.xlsx' template to collect the management data.

Maintained by Olivier Heller. Last updated 28 days ago.

1.9 match 4.88 score 4 scripts

bedapub

designit:Blocking and Randomization for Experimental Design

Intelligently assign samples to batches in order to reduce batch effects. Batch effects can have a significant impact on data analysis, especially when the assignment of samples to batches coincides with the contrast groups being studied. By defining a batch container and a scoring function that reflects the contrasts, this package allows users to assign samples in a way that minimizes the potential impact of batch effects on the comparison of interest. Among other functionality, we provide an implementation for OSAT score by Yan et al. (2012, <doi:10.1186/1471-2164-13-689>).

Maintained by Iakov I. Davydov. Last updated 4 months ago.

design-of-experiments randomization

1.3 match 8 stars 7.28 score 24 scripts

bricenocenti

tabxplor:User-Friendly Tables with Color Helpers for Data Exploration

Make it easy to deal with multiple cross-tables in data exploration, by creating them, manipulating them, and adding color helpers to highlight important informations (differences from totals, comparisons between lines or columns, contributions to variance, confidence intervals, odds ratios, etc.). All functions are pipe-friendly and render data frames which can be easily manipulated. In the same time, time-taking operations are done with 'data.table' to go faster with big dataframes. Tables can be exported with formats and colors to 'Excel', plot and html.

Maintained by Brice Nocenti. Last updated 8 days ago.

1.9 match 1 stars 4.73 score 12 scripts 1 dependents

bioc

ComplexHeatmap:Make Complex Heatmaps

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

Maintained by Zuguang Gu. Last updated 5 months ago.

software visualization sequencing clustering complex-heatmaps heatmap

0.5 match 1.3k stars 16.93 score 16k scripts 151 dependents

setempler

miscset:Miscellaneous Tools Set

A collection of miscellaneous methods to simplify various tasks, including plotting, data.frame and matrix transformations, environment functions, regular expression methods, and string and logical operations, as well as numerical and statistical tools. Most of the methods are simple but useful wrappers of common base R functions, which extend S3 generics or provide default values for important parameters.

Maintained by Sven E. Templer. Last updated 8 years ago.

miscellaneous cpp

2.0 match 1 stars 4.40 score 50 scripts

elilillyco

rfacts:R Interface to 'FACTS' on Unix-Like Systems

The 'rfacts' package is an R interface to the Fixed and Adaptive Clinical Trial Simulator ('FACTS') on Unix-like systems. It programmatically invokes 'FACTS' to run clinical trial simulations, and it aggregates simulation output data into tidy data frames. These capabilities provide end-to-end automation for large-scale simulation pipelines, and they enhance computational reproducibility. For more information on 'FACTS' itself, please visit <https://www.berryconsultants.com/software/>.

Maintained by William Michael Landau. Last updated 3 years ago.

clinical-trials facts simulation

1.8 match 7 stars 5.02 score 10 scripts

davidgohel

flextable:Functions for Tabular Reporting

Use a grammar for creating and customizing pretty tables. The following formats are supported: 'HTML', 'PDF', 'RTF', 'Microsoft Word', 'Microsoft PowerPoint' and R 'Grid Graphics'. 'R Markdown', 'Quarto' and the package 'officer' can be used to produce the result files. The syntax is the same for the user regardless of the type of output to be produced. A set of functions allows the creation, definition of cell arrangement, addition of headers or footers, formatting and definition of cell content with text and or images. The package also offers a set of high-level functions that allow tabular reporting of statistical models and the creation of complex cross tabulations.

Maintained by David Gohel. Last updated 1 months ago.

docx html5 ms-office-documents rmarkdown table

0.5 match 583 stars 17.04 score 7.3k scripts 119 dependents

kjhealy

gssrdoc:Document General Social Survey Variable

The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.

Maintained by Kieran Healy. Last updated 11 months ago.

3.8 match 2.28 score 38 scripts

uclahs-cds

CancerEvolutionVisualization:Publication Quality Phylogenetic Tree Plots

Generates tree plots with precise branch lengths, gene annotations, and cellular prevalence. The package handles complex tree structures (angles, lengths, etc.) and can be further refined as needed by the user.

Maintained by Paul Boutros. Last updated 2 days ago.

1.3 match 2 stars 6.34 score 5 scripts

luisdva

hexsession:Create a tile of logos for loaded packages

Creates a responsive HTML file with tiled hex logos for all loaded packages in a session, which can be saved as a static screenshot in png format.

Maintained by Luis D. Verde Arregoitia. Last updated 1 months ago.

2.0 match 35 stars 4.20 score 4 scripts

paballand

EconGeo:Computing Key Indicators of the Spatial Distribution of Economic Activities

Functions to compute a series of indices commonly used in the fields of economic geography, economic complexity, and evolutionary economics to describe the location, distribution, spatial organization, structure, and complexity of economic activities. Functions include basic spatial indicators such as the location quotient, the Krugman specialization index, the Herfindahl or the Shannon entropy indices but also more advanced functions to compute different forms of normalized relatedness between economic activities or network-based measures of economic complexity. Most of the functions use matrix calculus and are based on bipartite (incidence) matrices consisting of region - industry pairs.

Maintained by Pierre-Alexandre Balland. Last updated 2 years ago.

1.7 match 41 stars 4.96 score 44 scripts

hhwangbo

gainML:Machine Learning-Based Analysis of Potential Power Gain from Passive Device Installation on Wind Turbine Generators

Provides an effective machine learning-based tool that quantifies the gain of passive device installation on wind turbine generators. H. Hwangbo, Y. Ding, and D. Cabezon (2019) <arXiv:1906.05776>.

Maintained by Hoon Hwangbo. Last updated 6 years ago.

2.3 match 3.70 score 2 scripts

bioc

vsclust:Feature-based variance-sensitive quantitative clustering

Feature-based variance-sensitive clustering of omics data. Optimizes cluster assignment by taking into account individual feature variance. Includes several modules for statistical testing, clustering and enrichment analysis.

Maintained by Veit Schwammle. Last updated 2 months ago.

clustering annotation principalcomponent differentialexpression visualization proteomics metabolomics cpp

1.8 match 4.70 score 9 scripts

cran

apc:Age-Period-Cohort Analysis

Functions for age-period-cohort analysis. Aggregate data can be organised in matrices indexed by age-cohort, age-period or cohort-period. The data can include dose and response or just doses. The statistical model is a generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort factors. Individual-level data should have a row for each individual and columns for each of age, period, and cohort. The statistical model for repeated cross-section is a generalized linear model. The statistical model for panel data is ordinary least squares. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) <DOI:10.1093/biomet/asn026> is used. Thus, the analysis does not rely on ad hoc identification.

Maintained by Bent Nielsen. Last updated 4 years ago.

1.8 match 4.49 score 49 scripts

rmi-pacta

pacta.loanbook:Easily Install and Load PACTA for Banks Packages

PACTA (Paris Agreement Capital Transition Assessment) for Banks is a tool that allows banks to calculate the climate alignment of their corporate lending portfolios. This package is designed to make it easy to install and load multiple PACTA for Banks packages in a single step. It also provides thorough documentation - the PACTA for Banks cookbook at <https://rmi-pacta.github.io/pacta.loanbook/articles/cookbook_overview.html> - on how to run a PACTA for Banks analysis. This covers prerequisites for the analysis, the separate steps of running the analysis, the interpretation of PACTA for Banks results, and advanced use cases.

Maintained by Jacob Kastl. Last updated 3 days ago.

1.7 match 1 stars 4.68 score 12 scripts

pv71u98h1

m61r:Package About Data Manipulation in Pure Base R

Data manipulation in one package and in base R. Minimal. No dependencies. 'dplyr' and 'tidyr'-like in one place. Nothing else than base R to build the package.

Maintained by Jean-Marie Lepioufle. Last updated 5 months ago.

2.0 match 1 stars 4.00 score 5 scripts

sciviews

tabularise:Create Tabular Outputs from R

Create rich-formatted tabular outputs from R that can be incorporated into R Markdown/Quarto documents with correct output at least in HTML, LaTeX/PDF, Word and PowerPoint formats for various R objects.

Maintained by Philippe Grosjean. Last updated 9 months ago.

sciviews tabulation

1.8 match 4.56 score 12 scripts 4 dependents

bioc

SplicingFactory:Splicing Diversity Analysis for Transcriptome Data

The SplicingFactory R package uses transcript-level expression values to analyze splicing diversity based on various statistical measures, like Shannon entropy or the Gini index. These measures can quantify transcript isoform diversity within samples or between conditions. Additionally, the package analyzes the isoform diversity data, looking for significant changes between conditions.

Maintained by Endre Sebestyen. Last updated 5 months ago.

transcriptomics rnaseq differentialsplicing alternativesplicing transcriptomevariant gini-index rna-seq shannon-entropy simpson-index splicing

1.5 match 4 stars 5.20 score 1 scripts

kaiaragaki

gplate:A Grammar of Plates

`gplate` attempts to provide a succinct yet powerful grammar to describe common microwell layouts to aide in both plotting and tidying.

Maintained by Kai Aragaki. Last updated 7 months ago.

ggplot2

1.7 match 4 stars 4.56 score 9 scripts 3 dependents

alanarnholt

PASWR2:Probability and Statistics with R, Second Edition

Functions and data sets for the text Probability and Statistics with R, Second Edition.

Maintained by Alan T. Arnholt. Last updated 3 years ago.

1.8 match 1 stars 4.24 score 260 scripts

jensharbers

agricolaeplotr:Visualization of Design of Experiments from the 'agricolae' Package

Visualization of Design of Experiments from the 'agricolae' package with 'ggplot2' framework The user provides an experiment design from the 'agricolae' package, calls the corresponding function and will receive a visualization with 'ggplot2' based functions that are specific for each design. As there are many different designs, each design is tested on its type. The output can be modified with standard 'ggplot2' commands or with other packages with 'ggplot2' function extensions.

Maintained by Jens Harbers. Last updated 2 months ago.

1.2 match 8 stars 6.27 score 78 scripts

katilingban

ennet:Utilities to Extract and Analyse Text Data from the Emergency Nutrition Network Forum

The Emergency Nutrition Network or en-net forum is the go to online forum for field practitioners requiring prompt technical advice for operational challenges for which answers are not readily accessible in current guidelines. The questions and the corresponding answers raised within en-net can provide insight into what the key topics of discussion are within the nutrition sector. This package provides utility functions for the extraction, processing and analysis of text data from the online forum.

Maintained by Ernest Guevarra. Last updated 2 years ago.

en-net nutrition

3.6 match 2 stars 2.08 score 12 scripts

skranz

sktools:Helpful functions used in my courses

Several helpful functions that I use in my courses

Maintained by Sebastian Kranz. Last updated 4 years ago.

3.4 match 1 stars 2.15 score 28 scripts

repboxr

repboxMap:Mapping information from article and run supplement. Mainly (regression) tables.

This package should use as input only information stored in regdb tables.

Maintained by Sebastian Kranz. Last updated 1 months ago.

2.3 match 3.26 score 1 scripts 2 dependents

ceopinio

CEOdata:Datasets of the CEO (Centre d'Estudis d'Opinio) for Opinion Polls in Catalonia

Easy and convenient access to the datasets of the "Centre d'Estudis d'Opinio", the Catalan institution for polling and public opinion. The package uses the data stored in the servers of the CEO and returns it in a tidy format.

Maintained by Xavier Fernández-i-Marín. Last updated 2 years ago.

1.5 match 5 stars 4.88 score 4 scripts

archaeothommy

chronochrt:Creating Chronological Charts

Easy way to draw chronological charts from tables, aiming to include an intuitive environment for anyone new to R. Includes 'ggplot2' geoms and theme for chronological charts.

Maintained by Thomas Rose. Last updated 6 months ago.

1.8 match 4.00 score 6 scripts

bioc

PAA:PAA (Protein Array Analyzer)

PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.

Maintained by Michael Turewicz. Last updated 5 months ago.

classification microarray onechannel proteomics cpp

1.7 match 4.34 score 11 scripts

bioc

epistack:Heatmaps of Stack Profiles from Epigenetic Signals

The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest. epistack needs three different inputs: 1) a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a `GRanges` (easily obtained from `bigwig` or `bam` files). 2) a list of feature of interest, such as peaks or transcription start sites, provided as a `GRanges` (easily obtained from `gtf` or `bed` files). 3) a score to sort the features, such as peak height or gene expression value.

Maintained by DEVAILLY Guillaume. Last updated 5 months ago.

rnaseq preprocessing chipseq geneexpression coverage bioinformatics

1.3 match 6 stars 5.26 score 5 scripts

khliland

ER:Effect + Residual Modelling

Multivariate modeling of data after deflation of interfering effects. EF Mosleth et al. (2021) <doi:10.1038/s41598-021-82388-w> and EF Mosleth et al. (2020) <doi:10.1016/B978-0-12-409547-2.14882-6>.

Maintained by Kristian Hovde Liland. Last updated 2 years ago.

2.3 match 3.00 score 1 scripts

sustainscapes

AICcPermanova:Model Selection of PERMANOVA Models Using AICc

Provides tools for model selection and model averaging of PerMANOVA models using Akaike Information Criterion corrected for small sample sizes (AICc) and Information Theoretic criteria principles. The package is built around the PERMANOVA analysis from the 'vegan' package and provides a streamlined workflow for generating and comparing models, obtaining model weights, and summarizing results using model averaging approaches. The methods implemented in this package are based on the practical information- theoretic approach described by Burnham, K. P. and Anderson, D. R. (2002) (<doi:10.1007/b97636>).

Maintained by Derek Corcoran. Last updated 1 years ago.

1.8 match 3.70 score 9 scripts

alteryx

promote:Client for the 'Alteryx Promote' API

Deploy, maintain, and invoke predictive models using the 'Alteryx Promote' REST API. 'Alteryx Promote' is available at the URL: <https://www.alteryx.com/products/alteryx-promote>.

Maintained by Paul E. Promote. Last updated 6 years ago.

1.6 match 5 stars 4.14 score 11 scripts

jakubnowicki

fixtuRes:Mock Data Generator

Generate mock data in R using YAML configuration.

Maintained by Jakub Nowicki. Last updated 3 years ago.

fixtures mock-data mock-data-generator test-data-generator yaml-configuration

1.3 match 16 stars 4.98 score 12 scripts

bergsmat

wrangle:A Systematic Data Wrangling Idiom

Supports systematic scrutiny, modification, and integration of data. The function status() counts rows that have missing values in grouping columns (returned by na() ), have non-unique combinations of grouping columns (returned by dup() ), and that are not locally sorted (returned by unsorted() ). Functions enumerate() and itemize() give sorted unique combinations of columns, with or without occurrence counts, respectively. Function ignore() drops columns in x that are present in y, and informative() drops columns in x that are entirely NA; constant() returns values that are constant, given a key. Data that have defined unique combinations of grouping values behave more predictably during merge operations.

Maintained by Tim Bergsma. Last updated 5 months ago.

2.3 match 2 stars 2.91 score 41 scripts

fanhansen

creditmodel:Toolkit for Credit Modeling, Analysis and Visualization

Provides a highly efficient R tool suite for Credit Modeling, Analysis and Visualization.Contains infrastructure functionalities such as data exploration and preparation, missing values treatment, outliers treatment, variable derivation, variable selection, dimensionality reduction, grid search for hyper parameters, data mining and visualization, model evaluation, strategy analysis etc. This package is designed to make the development of binary classification models (machine learning based models as well as credit scorecard) simpler and faster. The references including: 1 Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard: Development and Implementation Using SAS; 2 Bezdek, James C.FCM: The fuzzy c-means clustering algorithm. Computers & Geosciences (0098-3004),<DOI:10.1016/0098-3004(84)90020-7>.

Maintained by Dongping Fan. Last updated 3 years ago.

1.9 match 4 stars 3.48 score 15 scripts

jmnolan9

rcollectadhd:Collection of Data Sets Containing ADHD Related Data

A collection of data sets relating to ADHD (Attention Deficit Hyperactivity Disorder) which have been sourced from other packages on CRAN or from publications on other websites such as Kaggle <http://www.kaggle.com/>.The package also includes some simple functions for analysing data sets. The data sets and descriptions of the data sets may differ from what is on CRAN or other source websites. The aim of this package is to bring together data sets from a variety of ADHD research publications. This package would be useful for those interested in finding out what research has been done on the topic of ADHD, or those interested in comparing the results from different existing works. I started this project because I wanted to put together a collection of the data sets relevant to ADHD research, which I have a personal interest in. This work was conducted with the support of my mentor within the Global Talent Mentoring platform. <https://globaltalentmentoring.org/>.

Maintained by John Nolan. Last updated 5 months ago.

6.4 match 1 stars 1.00 score

kos59125

naturalsort:Natural Ordering

Provides functions related to human natural ordering. It handles adjacent digits in a character sequence as a number so that natural sort function arranges a character vector by their numbers, not digit characters. It is typically seen when operating systems lists file names. For example, a sequence a-1.png, a-2.png, a-10.png looks naturally ordered because 1 < 2 < 10 and natural sort algorithm arranges so whereas general sort algorithms arrange it into a-1.png, a-10.png, a-2.png owing to their third and fourth characters.

Maintained by Kosei Abe. Last updated 9 years ago.

0.9 match 9 stars 6.86 score 201 scripts 19 dependents

thomaschln

snplinkage:Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>.

Maintained by Thomas Charlon. Last updated 4 months ago.

geneticvariability microarray snp

1.3 match 4.62 score 14 scripts

pdwaggoner

hdImpute:A Batch Process for High Dimensional Imputation

A correlation-based batch process for fast, accurate imputation for high dimensional missing data problems via chained random forests. See Waggoner (2023) <doi:10.1007/s00180-023-01325-9> for more on 'hdImpute', Stekhoven and Bühlmann (2012) <doi:10.1093/bioinformatics/btr597> for more on 'missForest', and Mayer (2022) <https://github.com/mayer79/missRanger> for more on 'missRanger'.

Maintained by Philip Waggoner. Last updated 2 months ago.

1.8 match 2 stars 3.41 score 13 scripts

bioc

clippda:A package for the clinical proteomic profiling data analysis

Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.

Maintained by Stephen Nyangoma. Last updated 5 months ago.

proteomics onechannel preprocessing differentialexpression multiplecomparison

1.8 match 3.30 score 2 scripts

dormancy1

lefko3:Historical and Ahistorical Population Projection Matrix Analysis

Complete analytical environment for the construction and analysis of matrix population models and integral projection models. Includes the ability to construct historical matrices, which are 2d matrices comprising 3 consecutive times of demographic information. Estimates both raw and function-based forms of historical and standard ahistorical matrices. It also estimates function-based age-by-stage matrices and raw and function-based Leslie matrices.

Maintained by Richard P. Shefferson. Last updated 4 days ago.

openblas cpp

1.8 match 3.30 score 11 scripts

greshamlab

vivaldi:Viral Variant Location and Diversity

Analysis of minor alleles in Illumina sequencing data of viral genomes. Functions in 'vivaldi' primarily operate on vcf files.

Maintained by David Gresham. Last updated 1 years ago.

1.2 match 3 stars 4.78 score 7 scripts

florianjansen

eHOF:Extended HOF (Huisman-Olff-Fresco) Models

Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman et al. 1993 Journal of Vegetation Science <doi:10.1111/jvs.12050>) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.

Maintained by Florian Jansen. Last updated 3 months ago.

1.8 match 3.16 score 24 scripts

rhedley

locaR:A Set of Tools for Sound Localization

A set of functions and tools to conduct acoustic source localization, as well as organize and check localization data and results. The localization functions implement the modified steered response power algorithm described by Cobos et al. (2010) <doi:10.1109/LSP.2010.2091502>.

Maintained by Richard Hedley. Last updated 2 years ago.

1.1 match 1 stars 4.78 score 24 scripts

shackett

romic:R for High-Dimensional Omic Data

Represents high-dimensional data as tables of features, samples and measurements, and a design list for tracking the meaning of individual variables. Using this format, filtering, normalization, and other transformations of a dataset can be carried out in a flexible manner. 'romic' takes advantage of these transformations to create interactive 'shiny' apps for exploratory data analysis such as an interactive heatmap.

Maintained by Sean Hackett. Last updated 1 years ago.

2.0 match 1 stars 2.70 score 10 scripts

bioc

gmoviz:Seamless visualization of complex genomic variations in GMOs and edited cell lines

Genetically modified organisms (GMOs) and cell lines are widely used models in all kinds of biological research. As part of characterising these models, DNA sequencing technology and bioinformatics analyses are used systematically to study their genomes. Therefore, large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge on representing all findings in an informative and concise manner. `gmoviz` provides users with an easy way to visualise and facilitate the explanation of complex genomic editing events on a larger, biologically-relevant scale.

Maintained by Kathleen Zeglinski. Last updated 5 months ago.

visualization sequencing geneticvariability genomicvariation coverage

1.3 match 4.30 score 9 scripts

gabrielshimizu

AgroR:Experimental Statistics and Graphics for Agricultural Sciences

Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi:10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootechnics, Food Science and related areas).

Maintained by Gabriel Danilo Shimizu. Last updated 11 months ago.

1.7 match 1 stars 3.11 score 173 scripts

bioc

plotgardener:Coordinate-Based Genomic Visualization Package for R

Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

Maintained by Nicole Kramer. Last updated 5 months ago.

visualization genomeannotation functionalgenomics genomeassembly hic cpp

0.5 match 308 stars 10.16 score 167 scripts 3 dependents

wraff

wrProteo:Proteomics Data Analysis Functions

Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data. Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted. Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format): MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>), Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>), ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>), MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>), OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>), ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>), Proline (Bouyssie et al 2020 <doi:10.1093/bioinformatics/btaa118>), AlphaPept (preprint Strauss et al <doi:10.1101/2021.07.23.453379>) and Wombat-P (Bouyssie et al 2023 <doi:10.1021/acs.jproteome.3c00636>. Meta-data provided by initial analysis software and/or in sdrf format can be integrated to the analysis. Quantitative proteomics measurements frequently contain multiple NA values, due to physical absence of given peptides in some samples, limitations in sensitivity or other reasons. Help is provided to inspect the data graphically to investigate the nature of NA-values via their respective replicate measurements and to help/confirm the choice of NA-replacement algorithms. Meta-data in sdrf-format (Perez-Riverol et al 2020 <doi:10.1021/acs.jproteome.0c00376>) or similar tabular formats can be imported and included. Missing values can be inspected and imputed based on the concept of NA-neighbours or other methods. Dedicated filtering and statistical testing using the framework of package 'limma' <doi:10.18129/B9.bioc.limma> can be run, enhanced by multiple rounds of NA-replacements to provide robustness towards rare stochastic events. Multi-species samples, as frequently used in benchmark-tests (eg Navarro et al 2016 <doi:10.1038/nbt.3685>, Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>), can be run with special options considering such sub-groups during normalization and testing. Subsequently, ROC curves (Hand and Till 2001 <doi:10.1023/A:1010920819831>) can be constructed to compare multiple analysis approaches. As detailed example the data-set from Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>) quantified by MaxQuant, ProteomeDiscoverer, and Proline is provided with a detailed analysis of heterologous spike-in proteins.

Maintained by Wolfgang Raffelsberger. Last updated 4 months ago.

1.3 match 3.67 score 17 scripts 1 dependents

bdhitt

binGroup2:Identification and Estimation using Group Testing

Methods for the group testing identification problem: 1) Operating characteristics (e.g., expected number of tests) for commonly used hierarchical and array-based algorithms, and 2) Optimal testing configurations for these same algorithms. Methods for the group testing estimation problem: 1) Estimation and inference procedures for an overall prevalence, and 2) Regression modeling for commonly used hierarchical and array-based algorithms.

Maintained by Brianna Hitt. Last updated 1 years ago.

openblas cpp

1.8 match 2.48 score 3 scripts 1 dependents

bioc

gtrellis:Genome Level Trellis Layout

Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.

Maintained by Zuguang Gu. Last updated 5 months ago.

software visualization sequencing

0.5 match 39 stars 8.24 score 37 scripts 1 dependents

skranz

rmdtools:Tools for RMarkdown

Tools for RMarkdown

Maintained by Sebastian Kranz. Last updated 4 years ago.

2.3 match 1 stars 1.78 score 6 scripts 2 dependents

kylebittinger

usedist:Distance Matrix Utilities

Functions to re-arrange, extract, and work with distances.

Maintained by Kyle Bittinger. Last updated 10 months ago.

0.6 match 14 stars 6.63 score 169 scripts 6 dependents

cran

binGroup:Evaluation and Experimental Design for Binomial Group Testing

Methods for estimation and hypothesis testing of proportions in group testing designs: methods for estimating a proportion in a single population (assuming sensitivity and specificity equal to 1 in designs with equal group sizes), as well as hypothesis tests and functions for experimental design for this situation. For estimating one proportion or the difference of proportions, a number of confidence interval methods are included, which can deal with various different pool sizes. Further, regression methods are implemented for simple pooling and matrix pooling designs. Methods for identification of positive items in group testing designs: Optimal testing configurations can be found for hierarchical and array-based algorithms. Operating characteristics can be calculated for testing configurations across a wide variety of situations.

Maintained by Frank Schaarschmidt. Last updated 7 years ago.

1.8 match 2.18 score

ecohealthalliance

ehallm:What the Package Does (Title Case)

More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.

Maintained by The package maintainer. Last updated 4 months ago.

1.8 match 1 stars 2.18 score

dwbapst

paleotree:Paleontological and Phylogenetic Analyses of Evolution

Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of fossil taxa using stratigraphic data. This package also contains a large number of likelihood functions for estimating sampling and diversification rates from different types of data available from the fossil record (e.g. range data, occurrence data, etc). paleotree users can also simulate diversification and sampling in the fossil record using the function simFossilRecord, which is a detailed simulator for branching birth-death-sampling processes composed of discrete taxonomic units arranged in ancestor-descendant relationships. Users can use simFossilRecord to simulate diversification in incompletely sampled fossil records, under various models of morphological differentiation (i.e. the various patterns by which morphotaxa originate from one another), and with time-dependent, longevity-dependent and/or diversity-dependent rates of diversification, extinction and sampling. Additional functions allow users to translate simulated ancestor-descendant data from simFossilRecord into standard time-scaled phylogenies or unscaled cladograms that reflect the relationships among taxon units.

Maintained by David W. Bapst. Last updated 8 months ago.

0.5 match 21 stars 7.53 score 216 scripts 2 dependents

luckinet

tabshiftr:Reshape Disorganised Messy Data

Helps the user to build and register schema descriptions of disorganised (messy) tables. Disorganised tables are tables that are not in a topologically coherent form, where packages such as 'tidyr' could be used for reshaping. The schema description documents the arrangement of input tables and is used to reshape them into a standardised (tidy) output format.

Maintained by Steffen Ehrmann. Last updated 30 days ago.

data-management data-reshaping schemas

0.5 match 6 stars 7.13 score 62 scripts 1 dependents

randy3k

iterpc:Efficient Iterator for Permutations and Combinations

Iterator for generating permutations and combinations. They can be either drawn with or without replacement, or with distinct/ non-distinct items (multiset). The generated sequences are in lexicographical order (dictionary order). The algorithms to generate permutations and combinations are memory efficient. These iterative algorithms enable users to process all sequences without putting all results in the memory at the same time. The algorithms are written in C/C++ for faster performance. Note: 'iterpc' is no longer being maintained. Users are recommended to switch to 'arrangements'.

Maintained by Randy Lai. Last updated 5 years ago.

0.5 match 9 stars 7.17 score 47 scripts 5 dependents

bioc

treeclimbR:An algorithm to find optimal signal levels in a tree

The arrangement of hypotheses in a hierarchical structure appears in many research fields and often indicates different resolutions at which data can be viewed. This raises the question of which resolution level the signal should best be interpreted on. treeclimbR provides a flexible method to select optimal resolution levels (potentially different levels in different parts of the tree), rather than cutting the tree at an arbitrary level. treeclimbR uses a tuning parameter to generate candidate resolutions and from these selects the optimal one.

Maintained by Charlotte Soneson. Last updated 3 months ago.

statisticalmethod cellbasedassays

0.5 match 20 stars 7.00 score 45 scripts

j-mitchel

scITD:Single-Cell Interpretable Tensor Decomposition

Single-cell Interpretable Tensor Decomposition (scITD) employs the Tucker tensor decomposition to extract multicell-type gene expression patterns that vary across donors/individuals. This tool is geared for use with single-cell RNA-sequencing datasets consisting of many source donors. The method has a wide range of potential applications, including the study of inter-individual variation at the population-level, patient sub-grouping/stratification, and the analysis of sample-level batch effects. Each "multicellular process" that is extracted consists of (A) a multi cell type gene loadings matrix and (B) a corresponding donor scores vector indicating the level at which the corresponding loadings matrix is expressed in each donor. Additional methods are implemented to aid in selecting an appropriate number of factors and to evaluate stability of the decomposition. Additional tools are provided for downstream analysis, including integration of gene set enrichment analysis and ligand-receptor analysis. Tucker, L.R. (1966) <doi:10.1007/BF02289464>. Unkel, S., Hannachi, A., Trendafilov, N. T., & Jolliffe, I. T. (2011) <doi:10.1007/s13253-011-0055-9>. Zhou, G., & Cichocki, A. (2012) <doi:10.2478/v10175-012-0051-4>.

Maintained by Jonathan Mitchel. Last updated 2 years ago.

cpp

1.8 match 1.98 score 19 scripts

hsonne

magickx:Extension of the R-Package magick

Image manipulation based on the magick package. It contains functions to select or remove horizontal or vertical stripes from an image. These may be used to cut off undesired areas from an image, e.g. as preparation for optical character recognition (OCR).

Maintained by Hauke Sonnenberg. Last updated 5 years ago.

2.0 match 1.70 score 1 scripts

cran

s2dv:A Set of Common Tools for Seasonal to Decadal Verification

The advanced version of package 's2dverification'. It is intended for 'seasonal to decadal' (s2d) climate forecast verification, but it can also be used in other kinds of forecasts or general climate analysis. This package is specially designed for the comparison between the experimental and observational datasets. The functionality of the included functions covers from data retrieval, data post-processing, skill scores against observation, to visualization. Compared to 's2dverification', 's2dv' is more compatible with the package 'startR', able to use multiple cores for computation and handle multi-dimensional arrays with a higher flexibility. The CDO version used in development is 1.9.8.

Maintained by Ariadna Batalla. Last updated 5 months ago.

1.7 match 1.95 score 3 dependents

gk-crop

sunscanimport:Imports data from sunscan device

Provides functions to import, convert and visualize LAI measurements from Sunscan device. An interactive shiny app is included.

Maintained by Gunther Krauss. Last updated 1 months ago.

data shiny

1.9 match 1.70 score

alistaire47

passport:Travel Smoothly Between Country Name and Code Formats

Smooths the process of working with country names and codes via powerful parsing, standardization, and conversion utilities arranged in a simple, consistent API. Country name formats include multiple sources including the Unicode Common Locale Data Repository (CLDR, <http://cldr.unicode.org/>) common-sense standardized names in hundreds of languages.

Maintained by Edward Visel. Last updated 4 years ago.

country-codes country-data country-names

0.5 match 35 stars 6.17 score 28 scripts 1 dependents

yannabraham

Radviz:Project Multidimensional Data in 2D Space

An implementation of the radviz projection in R. It enables the visualization of multidimensional data while maintaining the relation to the original dimensions. This package provides functions to create and plot radviz projections, and a number of summary plots that enable comparison and analysis. For reference see Ankerst *et al.* (1996) (<https://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.68.1811>) for original implementation, see Di Caro *et al* (2012) (<https://link.springer.com/chapter/10.1007/978-3-642-13672-6_13>) for the original method for dimensional anchor arrangements, see Demsar *et al.* (2007) (<doi:10.1016/j.jbi.2007.03.010>) for the original Freeviz implementation.

Maintained by Yann Abraham. Last updated 3 years ago.

high-dimensional-data radviz science visualization cpp

0.5 match 10 stars 6.19 score 52 scripts

datasketch

shinypanels:Shiny Layout with Collapsible Panels

Create 'Shiny Apps' with collapsible vertical panels. This package provides a new visual arrangement for elements on top of 'Shiny'. Use the expand and collapse capabilities to leverage web applications with many elements to focus the user attention on the panel of interest.

Maintained by Juan Pablo Marin Diaz. Last updated 9 months ago.

shiny

0.5 match 80 stars 6.01 score 43 scripts

thiyangtdata

MedLEA:Morphological and Structural Features of Medicinal Leaves

Contains a dataset of morphological and structural features of 'Medicinal LEAves (MedLEA)'. The features of each species is recorded by manually viewing the medicinal plant repository available at (<http://www.instituteofayurveda.org/plants/>). You can also download repository of leaf images of 1099 medicinal plants in Sri Lanka.

Maintained by Thiyanga S. Talagala. Last updated 2 years ago.

1.1 match 2.70 score 5 scripts

mikmart

ggragged:Ragged Grids for 'ggplot2'

Extend 'ggplot2' facets to panel layouts arranged in a grid with ragged edges. facet_ragged_rows() groups panels into rows that can vary in length, facet_ragged_cols() does the same but for columns. These can be useful, for example, to represent nested or partially crossed relationships between faceting variables.

Maintained by Mikko Marttila. Last updated 5 months ago.

0.5 match 35 stars 5.77 score 34 scripts

miyamot0

fxl:'fxl' Single Case Design Charting Package

The 'fxl' Charting package is used to prepare and design single case design figures that are typically prepared in spreadsheet software. With 'fxl', there is no need to leave the R environment to prepare these works and many of the more unique conventions in single case experimental designs can be performed without the need for physically constructing features of plots (e.g., drawing annotations across plots). Support is provided for various different plotting arrangements (e.g., multiple baseline), annotations (e.g., brackets, arrows), and output formats (e.g., svg, rasters).

Maintained by Shawn Gilroy. Last updated 3 months ago.

behavior-analysis single-case-design visual-analysis

0.5 match 8 stars 5.46 score 24 scripts

anla8000

AmpliconDuo:Statistical Analysis of Amplicon Data of the Same Sample to Identify Artefacts

Increasingly powerful techniques for high-throughput sequencing open the possibility to comprehensively characterize microbial communities, including rare species. However, a still unresolved issue are the substantial error rates in the experimental process generating these sequences. To overcome these limitations we propose an approach, where each sample is split and the same amplification and sequencing protocol is applied to both halves. This procedure should allow to detect likely PCR and sequencing artifacts, and true rare species by comparison of the results of both parts. The AmpliconDuo package, whereas amplicon duo from here on refers to the two amplicon data sets of a split sample, is intended to help interpret the obtained read frequency distribution across split samples, and to filter the false positive reads.

Maintained by Anja Lange. Last updated 5 years ago.

1.7 match 1.65 score 15 scripts

sgmmahon

hhmR:Hierarchical Heatmaps

Allows users to create high-quality heatmaps from labelled, hierarchical data. Specifically, for data with a two-level hierarchical structure, it will produce a heatmap where each row and column represents a category at the lower level. These rows and columns are then grouped by the higher-level group each category belongs to, with the names for each category and groups shown in the margins. While other packages (e.g. 'dendextend') allow heatmap rows and columns to be arranged by groups only, 'hhmR' also allows the labelling of the data at both the category and group level.

Maintained by Michael Mahony. Last updated 2 months ago.

0.5 match 4 stars 5.38 score 1 scripts

jsjuni

rollupTree:Perform Recursive Computations

Mass rollup for a Bill of Materials is an example of a class of computations in which elements are arranged in a tree structure and some property of each element is a computed function of the corresponding values of its child elements. Leaf elements, i.e., those with no children, have values assigned. In many cases, the combining function is simple arithmetic sum; in other cases (e.g., mass properties), the combiner may involve other information such as the geometric relationship between parent and child, or statistical relations such as root-sum-of-squares (RSS). This package implements a general function for such problems. It is adapted to specific recursive computations by functional programming techniques; the caller passes a function as the update parameter to rollup() (or, at a lower level, passes functions as the get, set, combine, and override parameters to update_prop()) at runtime to specify the desired operations. The implementation relies on graph-theoretic algorithms from the 'igraph' package of Csárdi, et al. (2006 <doi:10.5281/zenodo.7682609>).

Maintained by James Steven Jenkins. Last updated 11 days ago.

0.5 match 2 stars 5.32 score 1 dependents

chjackson

survextrap:Survival Extrapolation with a Flexible Parametric Model and External Data

Survival analysis using a flexible Bayesian model for individual-level right-censored data, optionally combined with aggregate data on counts of survivors in different periods of time. An M-spline is used to describe the hazard function, with a hierarchical prior on the coefficients to control overfitting. Proportional hazards or flexible non-proportional hazards models can be used to relate survival to predictors. Mixture cure models, additive hazards (relative survival) models and waning treatment effects models are also supported. Priors can be customised and calibrated to substantive beliefs. Posterior distributions are estimated using Stan, and outputs are arranged in a tidy format. See See Jackson (2023) <doi:10.48550/arXiv.2306.03957>.

Maintained by Christopher Jackson. Last updated 18 days ago.

cpp

0.5 match 10 stars 5.00 score 11 scripts