R-universe search: highlighting

hadley

highlight:Syntax Highlighter

Syntax highlighter for R code based on the results of the R parser. Rendering in HTML and latex markup. Custom Sweave driver performing syntax highlighting of R code chunks.

Maintained by Hadley Wickham. Last updated 2 years ago.

cpp

74.4 match 4.72 score 67 scripts 4 dependents

federiva

highlighter:Code Syntax Highlighting using the 'Prism.js' Library

Code Syntax Highlighting made easy for code snippets or complete files. Whether you're documenting your data analysis or creating interactive 'shiny' apps.

Maintained by Federico Rivadeneira. Last updated 1 years ago.

73.7 match 2 stars 4.18 score 15 scripts

r-lib

downlit:Syntax Highlighting and Automatic Linking

Syntax highlighting of R code, specifically designed for the needs of 'RMarkdown' packages like 'pkgdown', 'hugodown', and 'bookdown'. It includes linking of function calls to their documentation on the web, and automatic translation of ANSI escapes in output to the equivalent HTML.

Maintained by Hadley Wickham. Last updated 10 months ago.

syntax-highlighting

21.7 match 90 stars 12.72 score 364 scripts 176 dependents

yihui

highr:Syntax Highlighting for R Source Code

Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package (<https://gitlab.com/saalen/highlight>).

Maintained by Yihui Xie. Last updated 10 months ago.

html latex syntax-highlighting

15.2 match 47 stars 14.35 score 92 scripts 4.2k dependents

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.

8.8 match 983 stars 15.62 score 10k scripts 213 dependents

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 8 days ago.

docx html5 ms-office-documents rmarkdown table

7.6 match 582 stars 17.09 score 7.3k scripts 124 dependents

talgalili

dendextend:Extending 'dendrogram' Functionality in R

Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.

Maintained by Tal Galili. Last updated 2 months ago.

6.2 match 154 stars 17.13 score 6.0k scripts 165 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 4 months ago.

d3js data-visualization ggplot2 javascript plotly shiny webgl

5.1 match 2.6k stars 19.43 score 93k scripts 797 dependents

janmarvin

openxlsx2:Read, Write and Edit 'xlsx' Files

Simplifies the creation of 'xlsx' files by providing a high level interface to writing, styling and editing worksheets.

Maintained by Jan Marvin Garbuszus. Last updated 1 days ago.

xlsx cpp

7.1 match 139 stars 13.62 score 194 scripts 11 dependents

yutannihilation

gghighlight:Highlight Lines and Points in 'ggplot2'

Make it easier to explore data with highlights.

Maintained by Hiroaki Yutani. Last updated 7 months ago.

7.6 match 523 stars 11.64 score 1.6k scripts 4 dependents

yihui

knitr:A General-Purpose Package for Dynamic Report Generation in R

Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

Maintained by Yihui Xie. Last updated 13 hours ago.

dynamic-documents knitr literate-programming rmarkdown sweave

3.5 match 2.4k stars 23.64 score 116k scripts 4.2k dependents

coolbutuseless

emphatic:Exploratory Analysis of Tabular Data using Colour Highlighting

Tools for exploratory analysis of tabular data using colour highlighting. Highlighting is displayed in any console supporting 'ANSI' colours, and can be converted to 'HTML', 'typst', 'latex' and 'SVG'. 'quarto' and 'rmarkdown' rendering are directly supported. It is also possible to add colour to regular expression matches and highlight differences between two arbitrary R objects.

Maintained by Mike Cheng. Last updated 3 months ago.

10.9 match 140 stars 7.55 score 12 scripts

samuel-marsh

scCustomize:Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.

Maintained by Samuel Marsh. Last updated 3 months ago.

customization ggplot2 scrna-seq seurat single-cell single-cell-genomics single-cell-rna-seq visualization

9.8 match 246 stars 8.45 score 1.1k scripts

thomas-neitmann

ggcharts:Get You to Your Desired Plot Faster

Streamlines the creation of common charts by taking care of a lot of data preprocessing and plot customization for the user. Provides a high-level interface for creating plots using 'ggplot2'.

Maintained by Thomas Neitmann. Last updated 3 years ago.

data-visualization ggplot2 plots

9.4 match 291 stars 8.49 score 119 scripts 1 dependents

r-lib

cli:Helpers for Developing Command Line Interfaces

A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.

Maintained by Gábor Csárdi. Last updated 15 days ago.

cli

3.9 match 664 stars 19.34 score 1.4k scripts 14k dependents

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

11.3 match 68 stars 6.49 score 15 scripts

asgr

imager:Image Processing Library Based on 'CImg'

Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.

Maintained by Aaron Robotham. Last updated 8 days ago.

libx11 fftw3 tiff cpp openmp

5.2 match 17 stars 13.53 score 2.4k scripts 44 dependents

ropensci

osmplotr:Bespoke Images of 'OpenStreetMap' Data

Bespoke images of 'OpenStreetMap' ('OSM') data and data visualisation using 'OSM' objects.

Maintained by Mark Padgham. Last updated 1 months ago.

data-visualisation highlighting-clusters openstreetmap osm overpass overpass-api peer-reviewed

8.7 match 139 stars 7.97 score 80 scripts

kiendang

rdocsyntax:Syntax Highlighting for R HTML Documentation

Provides syntax highlighting for R HTML documentation.

Maintained by Trung Kien Dang. Last updated 11 months ago.

ace-editor documentation highlighting rstudio syntax-highlighting

22.8 match 21 stars 3.02 score 1 scripts

r-lib

prettycode:Pretty Print R Code in the Terminal

Replace the standard print method for functions with one that performs syntax highlighting, using ANSI colors, if the terminal supports them.

Maintained by Gábor Csárdi. Last updated 6 months ago.

9.4 match 102 stars 7.30 score 9 scripts 4 dependents

rachelesrogers

highlightr:Highlight Conserved Edits Across Versions of a Document

Input multiple versions of a source document, and receive HTML code for a highlighted version of the source document indicating the frequency of occurrence of phrases in the different versions. This method is described in Chapter 3 of Rogers (2024) <https://digitalcommons.unl.edu/dissertations/AAI31240449/>.

Maintained by Rachel Rogers. Last updated 6 months ago.

12.5 match 1 stars 5.28 score 16 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

7.4 match 209 stars 8.79 score 460 scripts 4 dependents

bioc

SBGNview:"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

SBGNview is a tool set for pathway based data visalization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview, with the following key features: 1. Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN); 2. Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP) and user defined pathways; 3. Covers 5,200 reference pathways and over 3,000 species by default; 4. Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight; 5. SBGN pathway data manipulation, processing, extraction and analysis.

Maintained by Weijun Luo. Last updated 5 months ago.

genetarget pathways graphandnetwork visualization genesetenrichment differentialexpression geneexpression microarray rnaseq genetics metabolomics proteomics systemsbiology sequencing

10.3 match 26 stars 6.23 score 22 scripts

kasperwelbers

tokenbrowser:Create Full Text Browsers from Annotated Token Lists

Create browsers for reading full texts from a token list format. Information obtained from text analyses (e.g., topic modeling, word scaling) can be used to annotate the texts.

Maintained by Kasper Welbers. Last updated 4 years ago.

cpp

10.9 match 7 stars 5.38 score 13 scripts 5 dependents

lindbrook

cholera:Amend, Augment and Aid Analysis of John Snow's Cholera Map

Amends errors, augments data and aids analysis of John Snow's map of the 1854 London cholera outbreak.

Maintained by lindbrook. Last updated 4 hours ago.

cholera data-visualization datasets epidemiology john-snow public-health triangulation-delaunay voronoi voronoi-polygons

5.8 match 134 stars 9.34 score 95 scripts

january3

colorDF:Colorful Data Frames in R Terminal

Colorful Data Frames in the terminal. The new class does change the behaviour of any of the objects, but adds a style definition and a print method. Using ANSI escape codes, it colors the terminal output of data frames. Some column types (such as p-values and identifiers) are automatically recognized.

Maintained by January Weiner. Last updated 3 years ago.

9.1 match 17 stars 5.64 score 51 scripts

trinker

sentimentr:Calculate Text Polarity Sentiment

Calculate text polarity sentiment at the sentence level and optionally aggregate by rows or grouping variable(s).

Maintained by Tyler Rinker. Last updated 3 years ago.

amplifier polarity sentiment sentiment-analysis valence-shifter

5.3 match 435 stars 9.60 score 680 scripts 2 dependents

johncoene

echarts4r:Create Interactive Graphs with 'Echarts JavaScript' Version 5

Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes 36 chart types, themes, 'Shiny' proxies and animations.

Maintained by David Munoz Tord. Last updated 18 days ago.

echarts hacktoberfest htmlwidget htmlwidgets visualization

4.3 match 603 stars 11.45 score 1.3k scripts 11 dependents

bioc

vidger:Create rapid visualizations of RNAseq data in R

The aim of vidger is to rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: Cuffdiff, DESeq2, and edgeR.

Maintained by Brandon Monier. Last updated 5 months ago.

immunooncology visualization rnaseq differentialexpression geneexpression data-munging differential-expression gene-expression rna-seq-analysis

7.2 match 19 stars 6.61 score 27 scripts

bioc

Gviz:Plotting data and annotation information along genomic coordinates

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

Maintained by Robert Ivanek. Last updated 5 months ago.

visualization microarray sequencing

3.3 match 79 stars 13.05 score 1.4k scripts 46 dependents

johncoene

cicerone:Provide Tours of 'Shiny' Applications

Provide step by step guided tours of 'Shiny' applications.

Maintained by John Coene. Last updated 2 months ago.

hacktoberfest shiny tour

5.6 match 190 stars 7.84 score 68 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

3.5 match 201 stars 11.66 score 2.4k scripts 5 dependents

polmine

polmineR:Verbs and Nouns for Corpus Analysis

Package for corpus analysis using the Corpus Workbench ('CWB', <https://cwb.sourceforge.io>) as an efficient back end for indexing and querying large corpora. The package offers functionality to flexibly create subcorpora and to carry out basic statistical operations (count, co-occurrences etc.). The original full text of documents can be reconstructed and inspected at any time. Beyond that, the package is intended to serve as an interface to packages implementing advanced statistical procedures. Respective data structures (document-term matrices, term-co-occurrence matrices etc.) can be created based on the indexed corpora.

Maintained by Andreas Blaette. Last updated 1 years ago.

5.2 match 49 stars 7.96 score 311 scripts

sssydysss

TransProR:Analysis and Visualization of Multi-Omics Data

A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10.1186/s13059-022-02648-4>), providing flexible and robust approaches to RNA-Seq data analysis. For more information, refer to the package vignettes and related publications.

Maintained by Dongyue Yu. Last updated 1 months ago.

5.3 match 190 stars 7.59 score 34 scripts

cderv

pandoc:Manage and Run Universal Converter 'Pandoc' from 'R'

Provides a set of tools to install, manage and run several 'Pandoc' versions.

Maintained by Christophe Dervieux. Last updated 1 years ago.

5.3 match 27 stars 7.17 score 194 scripts 3 dependents

sahirbhatnagar

manhattanly:Interactive Q-Q and Manhattan Plots Using 'plotly.js'

Create interactive manhattan, Q-Q and volcano plots that are usable from the R console, in 'Dash' apps, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a point to show details or drag a rectangle to zoom. A manhattan plot is a popular graphical method for visualizing results from high-dimensional data analysis such as a (epi)genome wide association study (GWAS or EWAS), in which p-values, Z-scores, test statistics are plotted on a scatter plot against their genomic position. Manhattan plots are used for visualizing potential regions of interest in the genome that are associated with a phenotype. Interactive manhattan plots allow the inspection of specific value (e.g. rs number or gene name) by hovering the mouse over a cell, as well as zooming into a region of the genome (e.g. a chromosome) by dragging a rectangle around the relevant area. This work is based on the 'qqman' package and the 'plotly.js' engine. It produces similar manhattan and Q-Q plots as the 'manhattan' and 'qq' functions in the 'qqman' package, with the advantage of including extra annotation information and interactive web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.

Maintained by Sahir Bhatnagar. Last updated 4 years ago.

5.1 match 60 stars 7.15 score 78 scripts

marce10

warbleR:Streamline Bioacoustic Analysis

Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and quantify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.

Maintained by Marcelo Araya-Salas. Last updated 2 months ago.

animal-acoustic-signals audio-processing bioacoustics spectrogram streamline-analysis cpp

3.3 match 56 stars 10.86 score 270 scripts 4 dependents

satijalab

Seurat:Tools for Single Cell Genomics

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Maintained by Paul Hoffman. Last updated 1 years ago.

human-cell-atlas single-cell-genomics single-cell-rna-seq cpp

2.0 match 2.4k stars 16.86 score 50k scripts 73 dependents

tidymodels

tidypredict:Run Predictions Inside the Database

It parses a fitted 'R' model object, and returns a formula in 'Tidy Eval' code that calculates the predictions. It works with several databases back-ends because it leverages 'dplyr' and 'dbplyr' for the final 'SQL' translation of the algorithm. It currently supports lm(), glm(), randomForest(), ranger(), earth(), xgb.Booster.complete(), cubist(), and ctree() models.

Maintained by Emil Hvitfeldt. Last updated 3 months ago.

dbplyr dplyr purrr rlang

3.0 match 262 stars 11.05 score 241 scripts 2 dependents

rstudio

rstudioapi:Safely Access the RStudio API

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

Maintained by Kevin Ushey. Last updated 5 months ago.

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

rstudio

rmarkdown:Dynamic Documents for R

Convert R Markdown documents into a variety of formats.

Maintained by Yihui Xie. Last updated 18 hours ago.

literate-programming markdown pandoc rmarkdown

1.5 match 2.9k stars 21.80 score 14k scripts 3.7k dependents

rstudio

dygraphs:Interface to 'Dygraphs' Interactive Time Series Charting Library

An R interface to the 'dygraphs' JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.

Maintained by Petr Shevtsov. Last updated 2 years ago.

2.4 match 365 stars 13.48 score 3.6k scripts 65 dependents

henrikbengtsson

aroma.affymetrix:Analysis of Large Affymetrix Microarray Data Sets

A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

infrastructure proprietaryplatforms exonarray microarray onechannel gui dataimport datarepresentation preprocessing qualitycontrol visualization reportwriting acgh copynumbervariants differentialexpression geneexpression snp transcription affymetrix analysis copy-number dna expression hpc large-scale notebook reproducibility rna

5.6 match 10 stars 5.79 score 112 scripts 3 dependents

rstudio

shiny:Web Application Framework for R

Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.

Maintained by Winston Chang. Last updated 6 days ago.

reactive rstudio shiny web-app web-development

1.5 match 5.5k stars 21.31 score 108k scripts 1.8k dependents

jokergoo

spiralize:Visualize Data on Spirals

It visualizes data along an Archimedean spiral <https://en.wikipedia.org/wiki/Archimedean_spiral>, makes so-called spiral graph or spiral chart. It has two major advantages for visualization: 1. It is able to visualize data with very long axis with high resolution. 2. It is efficient for time series data to reveal periodic patterns.

Maintained by Zuguang Gu. Last updated 10 months ago.

4.3 match 149 stars 7.37 score 35 scripts 3 dependents

bioc

MetCirc:Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data

MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectra object infrastructure defined in the package Spectra that stores MS/MS spectra. MetCirc offers functionality to calculate similarity between precursors based on the normalised dot product, neutral losses or user-defined functions and visualise similarities in a circular layout. Within the interactive framework the user can annotate MS/MS features based on their similarity to (known) related MS/MS features.

Maintained by Thomas Naake. Last updated 5 months ago.

shinyapps metabolomics massspectrometry visualization

8.9 match 3.48 score 3 scripts

rntq472

precisePlacement:Suite of Functions to Help Get Plot Elements Exactly Where You Want Them

Provides a selection of tools that make it easier to place elements onto a (base R) plot exactly where you want them. It allows users to identify points and distances on a plot in terms of inches, pixels, margin lines, data units, and proportions of the plotting space, all in a manner more simple than manipulating par().

Maintained by Jasper Watson. Last updated 4 years ago.

7.5 match 2 stars 4.00 score 10 scripts

bioc

EnhancedVolcano:Publication-ready volcano plots with enhanced colouring and labeling

Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations.

Maintained by Kevin Blighe. Last updated 5 months ago.

rnaseq geneexpression transcription differentialexpression immunooncology

2.4 match 427 stars 12.16 score 2.7k scripts 1 dependents

rstudio

DT:A Wrapper of the JavaScript Library 'DataTables'

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

Maintained by Joe Cheng. Last updated 4 months ago.

datatables htmlwidgets javascript shiny

1.5 match 604 stars 19.15 score 38k scripts 673 dependents

thinkr-open

remedy:'RStudio' Addins to Simplify 'Markdown' Writing

An 'RStudio' addin providing shortcuts for writing in 'Markdown'. This package provides a series of functions that allow the user to be more efficient when using 'Markdown'. For example, you can select a word, and put it in bold or in italics, or change the alignment of elements inside you Rmd. The idea is to map all the functionalities from 'remedy' on keyboard shortcuts, so that it provides an interface close to what you can find in any other text editor.

Maintained by Colin Fay. Last updated 5 years ago.

hacktoberfest

3.6 match 452 stars 7.83 score 50 scripts

r-lib

pkgdown:Make Static HTML Documentation for a Package

Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.

Maintained by Hadley Wickham. Last updated 13 days ago.

documentation-tool

1.5 match 734 stars 18.46 score 588 scripts 162 dependents

hzhanghenry

RCircos:Circos 2D Track Plot

A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.

Maintained by Hongen Zhang. Last updated 3 years ago.

3.8 match 6 stars 7.21 score 298 scripts 3 dependents

jinghuazhao

gap:Genetic Analysis Package

As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. <doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

Maintained by Jing Hua Zhao. Last updated 7 days ago.

genetics imputation lmm fortran

2.3 match 12 stars 11.94 score 448 scripts 16 dependents

rstudio

bookdown:Authoring Books and Technical Documents with R Markdown

Output formats and utilities for authoring books and technical documents with R Markdown.

Maintained by Yihui Xie. Last updated 17 days ago.

book bookdown epub gitbook html latex rmarkdown

1.5 match 3.9k stars 17.51 score 1.7k scripts 136 dependents

statistikat

VIM:Visualization and Imputation of Missing Values

New tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and allows to explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods. A graphical user interface available in the separate package VIMGUI allows an easy handling of the implemented plot methods.

Maintained by Matthias Templ. Last updated 8 months ago.

hotdeck imputation-methods model-predictions visualization cpp

1.8 match 85 stars 14.44 score 2.6k scripts 19 dependents

bioc

limma:Linear Models for Microarray and Omics Data

Data analysis, linear models and differential expression for omics data.

Maintained by Gordon Smyth. Last updated 3 days ago.

exonarray geneexpression transcription alternativesplicing differentialexpression differentialsplicing genesetenrichment dataimport bayesian clustering regression timecourse microarray micrornaarray mrnamicroarray onechannel proprietaryplatforms twochannel sequencing rnaseq batcheffect multiplecomparison normalization preprocessing qualitycontrol biomedicalinformatics cellbiology cheminformatics epigenetics functionalgenomics genetics immunooncology metabolomics proteomics systemsbiology transcriptomics

1.9 match 13.84 score 16k scripts 587 dependents

ropensci

prismjs:Server-Side Syntax Highlighting

Prism <https://prismjs.com/> is a lightweight, extensible syntax highlighter, built with modern web standards in mind. This package provides server-side rendering in R using 'V8' such that no JavaScript library is required in the resulting HTML documents. Over 400 languages are supported.

Maintained by Jeroen Ooms. Last updated 3 months ago.

5.6 match 5 stars 4.57 score 1 scripts 1 dependents

rapporter

pander:An R 'Pandoc' Writer

Contains some functions catching all messages, 'stdout' and other useful information while evaluating R code and other helpers to return user specified text elements (like: header, paragraph, table, image, lists etc.) in 'pandoc' markdown or several type of R objects similarly automatically transformed to markdown format. Also capable of exporting/converting (the resulting) complex 'pandoc' documents to e.g. HTML, 'PDF', 'docx' or 'odt'. This latter reporting feature is supported in brew syntax or with a custom reference class with a smarty caching 'backend'.

Maintained by Gergely Daróczi. Last updated 1 months ago.

literate-programming markdown pandoc pandoc-markdown reproducible-research rmarkdown cpp

1.5 match 298 stars 16.76 score 7.6k scripts 110 dependents

lindonkambule

gwaRs:Manhattan, Q-Q, and PCA Plots using 'ggplot2'

Generate Manhattan, Q-Q, and PCA plots from GWAS and PCA results using 'ggplot2'.

Maintained by Lindokuhle Nkambule. Last updated 4 years ago.

5.8 match 3 stars 4.18 score 4 scripts

r-lib

profvis:Interactive Visualizations for Profiling R Code

Interactive visualizations for profiling R code.

Maintained by Hadley Wickham. Last updated 6 months ago.

1.5 match 310 stars 15.64 score 1.3k scripts 153 dependents

lebebr01

highlightHTML:Highlight HTML Text and Tables

A tool to format R markdown with CSS ids for HTML output. The tool may be most helpful for those using markdown to create reproducible documents. The biggest limitations in formatting is the knowledge of CSS by the document authors.

Maintained by Brandon LeBeau. Last updated 4 years ago.

html markdown r-markdown

5.0 match 5 stars 4.74 score 22 scripts

hneth

unicol:The Colors of your University

Most universities use specific color combinations to express their unique brand identity. The 'unicol' package provides the colors and color palettes of various universities for easy plotting and printing in R. We collect and provide a diverse range of color palettes for creating scientific visualizations.

Maintained by Hansjoerg Neth. Last updated 8 months ago.

branding color color-palettes color-schemes corporate-design university-colors visual-identity

3.6 match 9 stars 6.58 score 10 scripts

bioc

escheR:Unified multi-dimensional visualizations with Gestalt principles

The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide this open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows.

Maintained by Boyi Guo. Last updated 5 months ago.

spatial singlecell transcriptomics visualization software multidimensional single-cell spatial-omics

3.5 match 6 stars 6.74 score 153 scripts 1 dependents

ropensci

rgbif:Interface to the Global Biodiversity Information Facility API

A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/developer/summary>). GBIF is a database of species occurrence records from sources all over the globe. rgbif includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the GBIF tile map service to make rasters summarizing huge amounts of data.

Maintained by John Waller. Last updated 19 days ago.

gbif specimens api web-services occurrences species taxonomy biodiversity data lifewatch oscibio spocc

1.8 match 161 stars 13.26 score 2.1k scripts 20 dependents

r-lib

covr:Test Coverage for Packages

Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' <https://about.codecov.io> or 'Coveralls' <https://coveralls.io>. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.

Maintained by Jim Hester. Last updated 2 months ago.

codecov coverage coverage-report travis-ci

1.5 match 337 stars 15.25 score 2.3k scripts 9 dependents

datastorm-open

visNetwork:Network Visualization using 'vis.js' Library

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

Maintained by Benoit Thieurmel. Last updated 2 years ago.

1.5 match 550 stars 15.25 score 4.1k scripts 196 dependents

mjskay

ggdist:Visualizations of Distributions and Uncertainty

Provides primitives for visualizing distributions using 'ggplot2' that are particularly tuned for visualizing uncertainty in either a frequentist or Bayesian mode. Both analytical distributions (such as frequentist confidence distributions or Bayesian priors) and distributions represented as samples (such as bootstrap distributions or Bayesian posterior samples) are easily visualized. Visualization primitives include but are not limited to: points with multiple uncertainty intervals, eye plots (Spiegelhalter D., 1999) <https://ideas.repec.org/a/bla/jorssa/v162y1999i1p45-58.html>, density plots, gradient plots, dot plots (Wilkinson L., 1999) <doi:10.1080/00031305.1999.10474474>, quantile dot plots (Kay M., Kola T., Hullman J., Munson S., 2016) <doi:10.1145/2858036.2858558>, complementary cumulative distribution function barplots (Fernandes M., Walls L., Munson S., Hullman J., Kay M., 2018) <doi:10.1145/3173574.3173718>, and fit curves with multiple uncertainty ribbons.

Maintained by Matthew Kay. Last updated 4 months ago.

ggplot2 uncertainty uncertainty-visualization visualization cpp

1.5 match 859 stars 14.95 score 3.1k scripts 62 dependents

lyzander

tableHTML:A Tool to Create HTML Tables

A tool to create and style HTML tables with CSS. These can be exported and used in any application that accepts HTML (e.g. 'shiny', 'rmarkdown', 'PowerPoint'). It also provides functions to create CSS files (which also work with shiny).

Maintained by Theo Boutaris. Last updated 2 years ago.

2.5 match 22 stars 9.10 score 280 scripts 2 dependents

bnosac

udpipe:Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the 'UDPipe' 'NLP' Toolkit

This natural language processing toolkit provides language-agnostic 'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency parsing' of raw text. Next to text parsing, the package also allows you to train annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided at <https://universaldependencies.org/format.html>. The techniques are explained in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0 with UDPipe', available at <doi:10.18653/v1/K17-3009>. The toolkit also contains functionalities for commonly used data manipulations on texts which are enriched with the output of the parser. Namely functionalities and algorithms for collocations, token co-occurrence, document term matrix handling, term frequency inverse document frequency calculations, information retrieval metrics (Okapi BM25), handling of multi-word expressions, keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntactical patterns) sentiment scoring and semantic similarity analysis.

Maintained by Jan Wijffels. Last updated 2 years ago.

conll dependency-parser lemmatization natural-language-processing nlp pos-tagging r-pkg rcpp text-mining tokenizer udpipe cpp

1.9 match 215 stars 11.83 score 1.2k scripts 9 dependents

isoverse

isoorbi:Process Orbitrap Isotopocule Data

Read and process isotopocule data from an Orbitrap Isotope Solutions mass spectrometer. Citation: Kantnerova et al. (Nature Protocols, 2024).

Maintained by Caj Neubauer. Last updated 8 months ago.

3.5 match 4 stars 6.31 score 17 scripts

bioc

maftools:Summarize, Analyze and Visualize MAF Files

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

Maintained by Anand Mayakonda. Last updated 5 months ago.

datarepresentation dnaseq visualization drivermutation variantannotation featureextraction classification somaticmutation sequencing functionalgenomics survival bioinformatics cancer-genome-atlas cancer-genomics genomics maf-files tcga curl bzip2 xz-utils zlib

1.5 match 461 stars 14.58 score 948 scripts 18 dependents

sachaepskamp

qgraph:Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation

Fork of qgraph - Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.

Maintained by Sacha Epskamp. Last updated 1 years ago.

cpp

1.9 match 69 stars 11.43 score 1.2k scripts 63 dependents

rnabioco

ggtrace:Trace and Highlight Groups of Data Points

Provides 'ggplot2' geoms that allow groups of data points to be outlined or highlighted for emphasis. This is particularly useful when working with dense datasets that are prone to overplotting.

Maintained by Ryan Sheridan. Last updated 1 years ago.

ggplot2 ggplot2-geom visualization

3.5 match 15 stars 6.06 score 38 scripts

rempsyc

rempsyc:Convenience Functions for Psychology

Make your workflow faster and easier. Easily customizable plots (via 'ggplot2'), nice APA tables (following the style of the *American Psychological Association*) exportable to Word (via 'flextable'), easily run statistical tests or check assumptions, and automatize various other tasks.

Maintained by Rémi Thériault. Last updated 2 months ago.

convenience-functions ggplot2 psychology statistics visualization

2.0 match 43 stars 10.68 score 214 scripts 2 dependents

mgondan

mathml:Translate R Expressions to 'MathML' and 'LaTeX'/'MathJax'

Translate R expressions to 'MathML' or 'MathJax'/'LaTeX' so that they can be rendered in R markdown documents and shiny apps. This package depends on R package 'rolog', which requires an installation of the 'SWI'-'Prolog' runtime either from 'swi-prolog.org' or from R package 'rswipl'.

Maintained by Matthias Gondan. Last updated 2 days ago.

3.3 match 4 stars 6.46 score 32 scripts

bauer-alex

APCtools:Routines for Descriptive and Model-Based APC Analysis

Age-Period-Cohort (APC) analyses are used to differentiate relevant drivers for long-term developments. The 'APCtools' package offers visualization techniques and general routines to simplify the workflow of an APC analysis. Sophisticated functions are available both for descriptive and regression model-based analyses. For the former, we use density (or ridgeline) matrices and (hexagonally binned) heatmaps as innovative visualization techniques building on the concept of Lexis diagrams. Model-based analyses build on the separation of the temporal dimensions based on generalized additive models, where a tensor product interaction surface (usually between age and period) is utilized to represent the third dimension (usually cohort) on its diagonal. Such tensor product surfaces can also be estimated while accounting for further covariates in the regression model. See Weigert et al. (2021) <doi:10.1177/1354816620987198> for methodological details.

Maintained by Alexander Bauer. Last updated 7 days ago.

3.5 match 14 stars 5.92 score 60 scripts

bioc

scDataviz:scDataviz: single cell dataviz and downstream analyses

In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need to improve data visualisation and to bring analysis capabilities to researchers even from non-technical backgrounds. scDataviz attempts to fit into this space, while also catering for advanced users. Additonally, due to the way that scDataviz is designed, which is based on SingleCellExperiment, it has a 'plug and play' feel, and immediately lends itself as flexibile and compatibile with studies that go beyond scDataviz. Finally, the graphics in scDataviz are generated via the ggplot engine, which means that users can 'add on' features to these with ease.

Maintained by Kevin Blighe. Last updated 5 months ago.

singlecell immunooncology rnaseq geneexpression transcription flowcytometry massspectrometry dataimport

3.2 match 63 stars 6.30 score 16 scripts

qile0317

APackOfTheClones:Visualization of Clonal Expansion for Single Cell Immune Profiles

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.

Maintained by Qile Yang. Last updated 4 months ago.

clonal-analysis immune-repertoire immune-system scrna-seq scrnaseq seurat single-cell single-cell-genomics cpp

3.1 match 15 stars 6.45 score 15 scripts

ropensci

RSelenium:R Bindings for 'Selenium WebDriver'

Provides a set of R bindings for the 'Selenium 2.0 WebDriver' (see <https://www.selenium.dev/documentation/> for more information) using the 'JsonWireProtocol' (see <https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol> for more information). 'Selenium 2.0 WebDriver' allows driving a web browser natively as a user would either locally or on a remote machine using the Selenium server it marks a leap forward in terms of web browser automation. Selenium automates web browsers (commonly referred to as browsers). Using RSelenium you can automate browsers locally or remotely.

Maintained by Jonathan Völkle. Last updated 2 years ago.

rselenium selenium webdriver

1.5 match 344 stars 13.38 score 1.9k scripts 12 dependents

kof-ch

tstools:A Time Series Toolbox for Official Statistics

Plot official statistics' time series conveniently: automatic legends, highlight windows, stacked bar chars with positive and negative contributions, sum-as-line option, two y-axes with automatic horizontal grids that fit both axes and other popular chart types. 'tstools' comes with a plethora of defaults to let you plot without setting an abundance of parameters first, but gives you the flexibility to tweak the defaults. In addition to charts, 'tstools' provides a super fast, 'data.table' backed time series I/O that allows the user to export / import long format, wide format and transposed wide format data to various file types.

Maintained by Stéphane Bisinger. Last updated 1 years ago.

3.1 match 11 stars 6.47 score 177 scripts

samhforbes

eyetrackingR:Eye-Tracking Data Analysis

Addresses tasks along the pipeline from raw data to analysis and visualization for eye-tracking data. Offers several popular types of analyses, including linear and growth curve time analyses, onset-contingent reaction time analyses, as well as several non-parametric bootstrapping approaches. For references to the approach see Mirman, Dixon & Magnuson (2008) <doi:10.1016/j.jml.2007.11.006>, and Barr (2008) <doi:10.1016/j.jml.2007.09.002>.

Maintained by Samuel Forbes. Last updated 2 years ago.

2.5 match 22 stars 7.84 score 60 scripts

bioc

scRepertoire:A toolkit for single-cell immune receptor profiling

scRepertoire is a toolkit for processing and analyzing single-cell T-cell receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use of 10x, AIRR, BD, MiXCR, Omniscope, TRUST4, and WAT3R single-cell formats. The functionality includes basic clonal analyses, repertoire summaries, distance-based clustering and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R workflows.

Maintained by Nick Borcherding. Last updated 12 days ago.

software immunooncology singlecell classification annotation sequencing cpp

1.9 match 327 stars 10.42 score 240 scripts

yulab-smu

TDbook:Companion Package for the Book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574, doi:10.1201/9781003279242)

The companion package that provides all the datasets used in the book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574, doi:10.1201/9781003279242).

Maintained by Guangchuang Yu. Last updated 3 years ago.

4.0 match 13 stars 4.88 score 59 scripts

fishr-core-team

FSA:Simple Fisheries Stock Assessment Methods

A variety of simple fish stock assessment methods.

Maintained by Derek H. Ogle. Last updated 2 months ago.

fish fisheries fisheries-management fisheries-stock-assessment population-dynamics stock-assessment

1.8 match 69 stars 11.16 score 1.7k scripts 6 dependents

bioc

GWASTools:Tools for Genome Wide Association Studies

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

Maintained by Stephanie M. Gogarten. Last updated 14 days ago.

snp geneticvariability qualitycontrol microarray

1.8 match 17 stars 10.67 score 396 scripts 5 dependents

bioc

EBImage:Image processing and analysis toolbox for R

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

Maintained by Andrzej Oleś. Last updated 5 months ago.

visualization bioinformatics image-analysis image-processing cpp

1.5 match 71 stars 12.77 score 1.5k scripts 33 dependents

frbcesab

chessboard:Create Network Connections Based on Chess Moves

Provides functions to work with directed (asymmetric) and undirected (symmetric) spatial networks. It makes the creation of connectivity matrices easier, i.e. a binary matrix of dimension n x n, where n is the number of nodes (sampling units) indicating the presence (1) or the absence (0) of an edge (link) between pairs of nodes. Different network objects can be produced by 'chessboard': node list, neighbor list, edge list, connectivity matrix. It can also produce objects that will be used later in Moran's Eigenvector Maps (Dray et al. (2006) <doi:10.1016/j.ecolmodel.2006.02.015>) and Asymetric Eigenvector Maps (Blanchet et al. (2008) <doi:10.1016/j.ecolmodel.2008.04.001>), methods available in the package 'adespatial' (Dray et al. (2023) <https://CRAN.R-project.org/package=adespatial>). This work is part of the FRB-CESAB working group Bridge <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/bridge/>.

Maintained by Nicolas Casajus. Last updated 1 years ago.

connectivity-matrix directed-networks neighborhood network one-dimensional-networks spatial-networks two-dimensional-networks undirected-networks

4.0 match 4 stars 4.78 score

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

1.9 match 186 stars 9.70 score 126 scripts 1 dependents

grunwaldlab

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

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

Maintained by Zachary Foster. Last updated 2 months ago.

community-diversity hierarchical metabarcoding pcr taxonomy trees cpp

1.9 match 140 stars 9.64 score 328 scripts

bioc

pRoloc:A unifying bioinformatics framework for spatial proteomics

The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.

Maintained by Lisa Breckels. Last updated 5 days ago.

immunooncology proteomics massspectrometry classification clustering qualitycontrol bioconductor proteomics-data spatial-proteomics visualisation openblas cpp

1.8 match 15 stars 10.31 score 101 scripts 2 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

rstudio

tfruns:Training Run Tools for 'TensorFlow'

Create and manage unique directories for each 'TensorFlow' training run. Provides a unique, time stamped directory for each run along with functions to retrieve the directory of the latest run or latest several runs.

Maintained by Tomasz Kalinowski. Last updated 12 months ago.

1.5 match 34 stars 11.80 score 325 scripts 77 dependents

bioc

marray:Exploratory analysis for two-color spotted microarray data

Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.

Maintained by Yee Hwa (Jean) Yang. Last updated 5 months ago.

microarray twochannel preprocessing

2.0 match 8.92 score 222 scripts 38 dependents

dreamrs

billboarder:Create Interactive Chart with the JavaScript 'Billboard' Library

Provides an 'htmlwidgets' interface to 'billboard.js', a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts. All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.

Maintained by Victor Perrier. Last updated 12 days ago.

data-visualization htmlwidgets

1.8 match 175 stars 9.70 score 96 scripts 4 dependents

r-lib

ymlthis:Write 'YAML' for 'R Markdown', 'bookdown', 'blogdown', and More

Write 'YAML' front matter for R Markdown and related documents. Work with 'YAML' objects more naturally and write the resulting 'YAML' to your clipboard or to 'YAML' files related to your project.

Maintained by Malcolm Barrett. Last updated 3 years ago.

1.8 match 165 stars 9.92 score 196 scripts 14 dependents

bioc

QDNAseq:Quantitative DNA Sequencing for Chromosomal Aberrations

Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

Maintained by Daoud Sie. Last updated 5 months ago.

copynumbervariation dnaseq genetics genomeannotation preprocessing qualitycontrol sequencing

1.7 match 49 stars 10.10 score 177 scripts 4 dependents

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

1.7 match 309 stars 10.17 score 167 scripts 3 dependents

mbtyers

riverdist:River Network Distance Computation and Applications

Reads river network shape files and computes network distances. Also included are a variety of computation and graphical tools designed for fisheries telemetry research, such as minimum home range, kernel density estimation, and clustering analysis using empirical k-functions with a bootstrap envelope. Tools are also provided for editing the river networks, meaning there is no reliance on external software.

Maintained by Matt Tyers. Last updated 5 months ago.

2.3 match 26 stars 7.50 score 96 scripts

diystat

NBPSeq:Negative Binomial Models for RNA-Sequencing Data

Negative Binomial (NB) models for two-group comparisons and regression inferences from RNA-Sequencing Data.

Maintained by Yanming Di. Last updated 11 years ago.

3.4 match 1 stars 4.88 score 17 scripts 3 dependents

aphalo

ggpp:Grammar Extensions to 'ggplot2'

Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to plots using native data coordinates, while geom_table_npc(), geom_plot_npc() and geom_grob_npc() do the same using "npc" coordinates through new aesthetics "npcx" and "npcy". Statistics: select observations based on 2D density. Positions: radial nudging away from a center point and nudging away from a line or curve; combined stacking and nudging; combined dodging and nudging.

Maintained by Pedro J. Aphalo. Last updated 1 months ago.

data-labels dataviz ggplot2-enhancements ggplot2-geoms ggplot2-insets ggplot2-positions

1.3 match 129 stars 12.53 score 582 scripts 26 dependents

dgrun

RaceID:Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <DOI:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <DOI:10.1186/s13059-023-02974-1>).

Maintained by Dominic Grün. Last updated 4 months ago.

cpp

3.5 match 4.74 score 110 scripts

jrowen

rhandsontable:Interface to the 'Handsontable.js' Library

An R interface to the 'Handsontable' JavaScript library, which is a minimalist Excel-like data grid editor. See <https://handsontable.com/> for details.

Maintained by Jonathan Owen. Last updated 3 years ago.

handsontable htmlwidgets javascript shiny sparkline

1.3 match 389 stars 12.31 score 1.0k scripts 46 dependents

bluefoxr

COINr:Composite Indicator Construction and Analysis

A comprehensive high-level package, for composite indicator construction and analysis. It is a "development environment" for composite indicators and scoreboards, which includes utilities for construction (indicator selection, denomination, imputation, data treatment, normalisation, weighting and aggregation) and analysis (multivariate analysis, correlation plotting, short cuts for principal component analysis, global sensitivity analysis, and more). A composite indicator is completely encapsulated inside a single hierarchical list called a "coin". This allows a fast and efficient work flow, as well as making quick copies, testing methodological variations and making comparisons. It also includes many plotting options, both statistical (scatter plots, distribution plots) as well as for presenting results.

Maintained by William Becker. Last updated 2 months ago.

1.8 match 26 stars 8.94 score 73 scripts 1 dependents

hneth

unikn:Graphical Elements of the University of Konstanz's Corporate Design

Define and use graphical elements of corporate design manuals in R. The 'unikn' package provides color functions (by defining dedicated colors and color palettes, and commands for finding, changing, viewing, and using them) and styled text elements (e.g., for marking, underlining, or plotting colored titles). The pre-defined range of colors and text decoration functions is based on the corporate design of the University of Konstanz <https://www.uni-konstanz.de/>, but can be adapted and extended for other purposes or institutions.

Maintained by Hansjoerg Neth. Last updated 4 months ago.

branding color color-palette colorscheme corporate-design palette text-decoration university-colors visual-identity

1.8 match 39 stars 8.77 score 156 scripts 2 dependents

erocoar

ggpol:Visualizing Social Science Data with 'ggplot2'

A 'ggplot2' extension for implementing parliament charts and several other useful visualizations.

Maintained by Frederik Tiedemann. Last updated 3 years ago.

dataviz ggplot-extension ggplot2 visualization

2.3 match 104 stars 7.00 score 212 scripts 1 dependents

michellekendall

phyloTop:Calculating Topological Properties of Phylogenies

Tools for calculating and viewing topological properties of phylogenetic trees.

Maintained by Michelle Kendall. Last updated 2 years ago.

4.1 match 1 stars 3.80 score 63 scripts

tomkellygenetics

vioplot:Violin Plot

A violin plot is a combination of a box plot and a kernel density plot. This package allows extensive customisation of violin plots.

Maintained by S. Thomas Kelly. Last updated 1 months ago.

boxplot colours customisation dataviz formula plotting violin-plot violinplot vioplot

1.3 match 27 stars 12.46 score 2.0k scripts 7 dependents

clementcalenge

adehabitatLT:Analysis of Animal Movements

A collection of tools for the analysis of animal movements.

Maintained by Clement Calenge. Last updated 7 months ago.

1.8 match 6 stars 8.60 score 370 scripts 12 dependents

ropensci

ritis:Integrated Taxonomic Information System Client

An interface to the Integrated Taxonomic Information System ('ITIS') (<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST API methods (<https://www.itis.gov/ws_description.html>), as well as the 'Solr' web service (<https://www.itis.gov/solr_documentation.html>).

Maintained by Julia Blum. Last updated 2 months ago.

taxonomy biology nomenclature json api web api-client identifiers species names api-wrapper itis taxize

2.0 match 16 stars 7.72 score 64 scripts 24 dependents

thinkr-open

papillon:Build And Highlight Package Documentation With Customized Templates

Helps creating company visual identity. Build your templates for your package vignettes, reports with {bookdown}, package presentation with {pkgdown}. Highlight your documentation in your projects. Allow for code folding.

Maintained by Sébastien Rochette. Last updated 2 years ago.

3.4 match 11 stars 4.34 score 4 scripts

bioc

monocle:Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.

Maintained by Cole Trapnell. Last updated 5 months ago.

immunooncology sequencing rnaseq geneexpression differentialexpression infrastructure dataimport datarepresentation visualization clustering multiplecomparison qualitycontrol cpp

1.7 match 8.71 score 1.6k scripts 2 dependents

jes-n

shinySearchbar:Shiny Searchbar - An Input Widget for Highlighting Text and More

Add a searchbar widget to your 'Shiny' application. The widget quickly integrates with any existing element containing text to highlight matches. Highlighting is done with the 'JavaScript' library 'mark.js'. The widget includes buttons to cycle through multiple instances of the match and automatically scroll to the matches in an overflow element (or window). The widget also displays the total number of matches and which match is currently being cycled through. The widget is structured as a 'Bootstrap 3' input group.

Maintained by Jesse Norris. Last updated 5 years ago.

3.7 match 15 stars 3.88 score 6 scripts

cardiomoon

autoReg:Automatic Linear and Logistic Regression and Survival Analysis

Make summary tables for descriptive statistics and select explanatory variables automatically in various regression models. Support linear models, generalized linear models and cox-proportional hazard models. Generate publication-ready tables summarizing result of regression analysis and plots. The tables and plots can be exported in "HTML", "pdf('LaTex')", "docx('MS Word')" and "pptx('MS Powerpoint')" documents.

Maintained by Keon-Woong Moon. Last updated 1 years ago.

2.0 match 49 stars 7.13 score 69 scripts

bioc

immunogenViewer:Visualization and evaluation of protein immunogens

Plots protein properties and visualizes position of peptide immunogens within protein sequence. Allows evaluation of immunogens based on structural and functional annotations to infer suitability for antibody-based methods aiming to detect native proteins.

Maintained by Katharina Waury. Last updated 2 months ago.

featureextraction proteomics software visualization

3.0 match 4.65 score 10 scripts

merck

metalite.ae:Adverse Events Analysis Using 'metalite'

Analyzes adverse events in clinical trials using the 'metalite' data structure. The package simplifies the workflow to create production-ready tables, listings, and figures discussed in the adverse events analysis chapters of "R for Clinical Study Reports and Submission" by Zhang et al. (2022) <https://r4csr.org/>.

Maintained by Yujie Zhao. Last updated 2 months ago.

cdisc clinical-trials metadata

1.5 match 18 stars 9.45 score 31 scripts 2 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 2 months ago.

1.5 match 13 stars 9.43 score 350 scripts 16 dependents

heraldoborges

STMotif:Discovery of Motifs in Spatial-Time Series

Allow to identify motifs in spatial-time series. A motif is a previously unknown subsequence of a (spatial) time series with relevant number of occurrences. For this purpose, the Combined Series Approach (CSA) is used.

Maintained by Heraldo Borges. Last updated 4 years ago.

3.4 match 2 stars 4.08 score 12 scripts

mlverse

chattr:Interact with Large Language Models in 'RStudio'

Enables user interactivity with large-language models ('LLM') inside the 'RStudio' integrated development environment (IDE). The user can interact with the model using the 'shiny' app included in this package, or directly in the 'R' console. It comes with back-ends for 'OpenAI', 'GitHub' 'Copilot', and 'LlamaGPT'.

Maintained by Edgar Ruiz. Last updated 2 months ago.

1.3 match 224 stars 10.36 score 71 scripts 1 dependents

reconhub

incidence:Compute, Handle, Plot and Model Incidence of Dated Events

Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

Maintained by Tim Taylor. Last updated 8 months ago.

outbreak

1.1 match 58 stars 12.06 score 504 scripts 11 dependents

trinker

numform:Tools to Format Numbers for Publication

Format numbers and plots for publication; includes the removal of leading zeros, standardization of number of digits, addition of affixes, and a p-value formatter. These tools combine the functionality of several 'base' functions such as 'paste()', 'format()', and 'sprintf()' into specific use case functions that are named in a way that is consistent with usage, making their names easy to remember and easy to deploy.

Maintained by Tyler Rinker. Last updated 3 years ago.

number-formating

2.3 match 51 stars 6.06 score 151 scripts 1 dependents

cran

rtsplot:Time Series Plot

A fast and elegant time series visualization package. In addition to the standard R plot types, this package supports candle sticks, open-high-low-close, and volume plots. Useful for visualizing any time series data, e.g., stock prices and technical indicators.

Maintained by Irina Kapler. Last updated 2 years ago.

8.0 match 1 stars 1.70 score

statnet

tsna:Tools for Temporal Social Network Analysis

Temporal SNA tools for continuous- and discrete-time longitudinal networks having vertex, edge, and attribute dynamics stored in the 'networkDynamic' format. This work was supported by grant R01HD68395 from the National Institute of Health.

Maintained by Skye Bender-deMoll. Last updated 1 years ago.

1.8 match 7 stars 7.65 score 93 scripts 2 dependents

bioc

PhyloProfile:PhyloProfile

PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.

Maintained by Vinh Tran. Last updated 10 days ago.

software visualization datarepresentation multiplecomparison functionalprediction dimensionreduction bioinformatics heatmap interactive-visualizations orthologs phylogenetic-profile shiny

1.7 match 33 stars 7.79 score 10 scripts

johncoene

sigmajs:Interface to 'Sigma.js' Graph Visualization Library

Interface to 'sigma.js' graph visualization library including animations, plugins and shiny proxies.

Maintained by John Coene. Last updated 4 years ago.

htmlwidgets network-visualization sigmajs

2.3 match 72 stars 5.92 score 77 scripts

barryzee

clickableImageMap:Implement 'tableGrob' Object as a Clickable Image Map

Implement 'tableGrob' object as a clickable image map. The 'clickableImageMap' package is designed to be more convenient and more configurable than the edit() function. Limitations that I have encountered with edit() are cannot control (1) positioning (2) size (3) appearance and formatting of fonts In contrast, when the table is implemented as a 'tableGrob', all of these features are controllable. In particular, the 'ggplot2' grid system allows exact positioning of the table relative to other graphics etc.

Maintained by Barry Zeeberg. Last updated 11 months ago.

6.6 match 2.00 score

tjmahr

solarizeddocx:A 'Solarized' Theme for 'RMarkdown` `Docx` Documents

An 'RMarkdown' output format for 'Microsoft' Word '.docx' documents created by 'pandoc'.

Maintained by Tristan Mahr. Last updated 3 years ago.

5.1 match 7 stars 2.54 score 1 scripts

r-lib

crayon:Colored Terminal Output

The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.

Maintained by Gábor Csárdi. Last updated 6 months ago.

0.8 match 324 stars 16.61 score 1.5k scripts 6.0k dependents

zwdzwd

wheatmap:Incrementally Build Complex Plots using Natural Semantics

Builds complex plots, heatmaps in particular, using natural semantics. Bigger plots can be assembled using directives such as 'LeftOf', 'RightOf', 'TopOf', and 'Beneath' and more. Other features include clustering, dendrograms and integration with 'ggplot2' generated grid objects. This package is particularly designed for bioinformaticians to assemble complex plots for publication.

Maintained by Wanding Zhou. Last updated 3 years ago.

2.0 match 10 stars 6.35 score 50 scripts 3 dependents

lakshay-anand

chromoMap:Interactive Genomic Visualization of Biological Data

Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors which can be highly advantageous in the scientific interpretations and research work. Because of the large size of the chromosomes, it is impractical to visualize each element on the same plot. However, the plot provides a magnified view for each of chromosome locus to render additional information and visualization specific for that location. You can map thousands of genes and can view all mappings easily. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order. The package provide multiple features like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling. The plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R 'Shiny' applications.

Maintained by Lakshay Anand. Last updated 3 years ago.

2.8 match 9 stars 4.46 score 80 scripts

flr

FLasher:Projection and Forecasting of Fish Populations, Stocks and Fleets

Projection of future population and fishery dynamics is carried out for a given set of management targets. A system of equations is solved, using Automatic Differentation (AD), for the levels of effort by fishery (fleet) that will result in the required abundances, catches or fishing mortalities.

Maintained by Iago Mosqueira. Last updated 25 days ago.

forecast fisheries flr cpp

1.8 match 2 stars 6.86 score 254 scripts 6 dependents

rstudio

reactlog:Reactivity Visualizer for 'shiny'

Building interactive web applications with R is incredibly easy with 'shiny'. Behind the scenes, 'shiny' builds a reactive graph that can quickly become intertwined and difficult to debug. 'reactlog' (Schloerke 2019) <doi:10.5281/zenodo.2591517> provides a visual insight into that black box of 'shiny' reactivity by constructing a directed dependency graph of the application's reactive state at any time point in a reactive recording.

Maintained by Barret Schloerke. Last updated 3 years ago.

1.5 match 125 stars 8.15 score 263 scripts

bioc

synergyfinder:Calculate and Visualize Synergy Scores for Drug Combinations

Efficient implementations for analyzing pre-clinical multiple drug combination datasets. It provides efficient implementations for 1.the popular synergy scoring models, including HSA, Loewe, Bliss, and ZIP to quantify the degree of drug combination synergy; 2. higher order drug combination data analysis and synergy landscape visualization for unlimited number of drugs in a combination; 3. statistical analysis of drug combination synergy and sensitivity with confidence intervals and p-values; 4. synergy barometer for harmonizing multiple synergy scoring methods to provide a consensus metric of synergy; 5. evaluation of synergy and sensitivity simultaneously to provide an unbiased interpretation of the clinical potential of the drug combinations. Based on this package, we also provide a web application (http://www.synergyfinder.org) for users who prefer graphical user interface.

Maintained by Shuyu Zheng. Last updated 5 months ago.

software statisticalmethod

2.3 match 5.42 score 44 scripts

adriancorrendo

soiltestcorr:Soil Test Correlation and Calibration

A compilation of functions designed to assist users on the correlation analysis of crop yield and soil test values. Functions to estimate crop response patterns to soil nutrient availability and critical soil test values using various approaches such as: 1) the modified arcsine-log calibration curve (Correndo et al. (2017) <doi:10.1071/CP16444>); 2) the graphical Cate-Nelson quadrants analysis (Cate & Nelson (1965)), 3) the statistical Cate-Nelson quadrants analysis (Cate & Nelson (1971) <doi:10.2136/sssaj1971.03615995003500040048x>), 4) the linear-plateau regression (Anderson & Nelson (1975) <doi:10.2307/2529422>), 5) the quadratic-plateau regression (Bullock & Bullock (1994) <doi:10.2134/agronj1994.00021962008600010033x>), and 6) the Mitscherlich-type exponential regression (Melsted & Peck (1977) <doi:10.2134/asaspecpub29.c1>). The package development stemmed from ongoing work with the Fertilizer Recommendation Support Tool (FRST) and Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification (SIIL) projects.

Maintained by Adrian A. Correndo. Last updated 9 months ago.

2.0 match 8 stars 6.09 score 31 scripts

sysbiolab

PathwaySpace:Spatial Projection of Network Signals along Geodesic Paths

For a given graph containing vertices, edges, and a signal associated with the vertices, the 'PathwaySpace' package performs a convolution operation, which involves a weighted combination of neighboring vertices and their associated signals. The package then uses a decay function to project these signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' could have various applications, such as visualizing and analyzing network data in a graphical format that highlights the relationships and signal strengths between vertices. It can be particularly useful for understanding the influence of signals through complex networks. By combining graph theory, signal processing, and visualization, the 'PathwaySpace' package provides a novel way of representing and analyzing graph data.

Maintained by Mauro Castro. Last updated 3 months ago.

bioinformatics biological-networks graph

2.5 match 2 stars 4.85 score 5 scripts

shwilks

r3js:'WebGL'-Based 3D Plotting using the 'three.js' Library

Provides R and 'JavaScript' functions to allow 'WebGL'-based 3D plotting using the 'three.js' 'JavaScript' library. Interactivity through roll-over highlighting and toggle buttons is also supported.

Maintained by Sam Wilks. Last updated 5 months ago.

3d-graphics plotting

2.0 match 14 stars 5.99 score 47 scripts

gshs-ornl

wbstats:Programmatic Access to Data and Statistics from the World Bank API

Search and download data from the World Bank Data API.

Maintained by Jesse Piburn. Last updated 4 years ago.

open-data world-bank world-bank-api worldbank

1.2 match 126 stars 10.07 score 1.1k scripts 3 dependents

jakobbossek

grapherator:A Modular Multi-Step Graph Generator

Set of functions for step-wise generation of (weighted) graphs. Aimed for research in the field of single- and multi-objective combinatorial optimization. Graphs are generated adding nodes, edges and weights. Each step may be repeated multiple times with different predefined and custom generators resulting in high flexibility regarding the graph topology and structure of edge weights.

Maintained by Jakob Bossek. Last updated 4 years ago.

combinatorial-optimization graph-generator minimum-spanning-tree multi-objective-optimization optimization

2.0 match 9 stars 6.04 score 27 scripts 1 dependents

yonicd

details:Create Details HTML Tag for Markdown and Package Documentation

Create a details HTML tag around R objects to place in a Markdown, 'Rmarkdown' and 'roxygen2' documentation.

Maintained by Jonathan Sidi. Last updated 2 months ago.

html markdown rmarkdown

1.3 match 83 stars 8.92 score 192 scripts 3 dependents

r-forge

CHNOSZ:Thermodynamic Calculations and Diagrams for Geochemistry

An integrated set of tools for thermodynamic calculations in aqueous geochemistry and geobiochemistry. Functions are provided for writing balanced reactions to form species from user-selected basis species and for calculating the standard molal properties of species and reactions, including the standard Gibbs energy and equilibrium constant. Calculations of the non-equilibrium chemical affinity and equilibrium chemical activity of species can be portrayed on diagrams as a function of temperature, pressure, or activity of basis species; in two dimensions, this gives a maximum affinity or predominance diagram. The diagrams have formatted chemical formulas and axis labels, and water stability limits can be added to Eh-pH, oxygen fugacity- temperature, and other diagrams with a redox variable. The package has been developed to handle common calculations in aqueous geochemistry, such as solubility due to complexation of metal ions, mineral buffers of redox or pH, and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ also implements a group additivity algorithm for the standard thermodynamic properties of proteins.

Maintained by Jeffrey Dick. Last updated 24 days ago.

fortran

1.3 match 9.46 score 238 scripts 4 dependents

microsoft

wpa:Tools for Analysing and Visualising Viva Insights Data

Opinionated functions that enable easier and faster analysis of Viva Insights data. There are three main types of functions in 'wpa': (i) Standard functions create a 'ggplot' visual or a summary table based on a specific Viva Insights metric; (2) Report Generation functions generate HTML reports on a specific analysis area, e.g. Collaboration; (3) Other miscellaneous functions cover more specific applications (e.g. Subject Line text mining) of Viva Insights data. This package adheres to 'tidyverse' principles and works well with the pipe syntax. 'wpa' is built with the beginner-to-intermediate R users in mind, and is optimised for simplicity.

Maintained by Martin Chan. Last updated 4 months ago.

workplace-analytics

1.8 match 30 stars 6.68 score 39 scripts 1 dependents

thomaschln

sgraph:Network Visualization Using 'sigma.js'

Interactive visualizations of graphs created with the 'igraph' package using a 'htmlwidgets' wrapper for the 'sigma.js' network visualization v2.4.0 <https://www.sigmajs.org/>, enabling to display several thousands of nodes. While several 'R' packages have been developed to interface 'sigma.js', all were developed for v1.x.x and none have migrated to v2.4.0 nor are they planning to. This package builds upon the 'sigmaNet' package, and users familiar with it will recognize the similar design approach. Two extensions have been added to the classic 'sigma.js' visualizations by overriding the underlying 'JavaScript' code, enabling to draw a frame around node labels, and to display labels on multiple lines by parsing line breaks. Other additional functionalities that did not require overriding 'sigma.js' code include toggling node visibility when clicked using a node attribute and highlighting specific edges. 'sigma.js' is currently preparing a stable release v3.0.0, and this package plans to update to it when it is available.

Maintained by Thomas Charlon. Last updated 4 months ago.

2.3 match 5.02 score 1 scripts 1 dependents

dwinter

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

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

Maintained by David Winter. Last updated 4 years ago.

1.7 match 71 stars 6.73 score 75 scripts

canmod

iidda.analysis:Tools for Analyzing IIDDA Datasets

This package contains tools for working with data obtained from the International Infectious Disease Data Archive.

Maintained by Steven Walker. Last updated 4 months ago.

2.0 match 5.60 score 23 scripts

skranz

RTutor:Interactive R problem sets with automatic testing of solutions and automatic hints

Interactive R problem sets with automatic testing of solutions and automatic hints

Maintained by Sebastian Kranz. Last updated 1 years ago.

economics learn-to-code problem-set rstudio rtutor shiny teaching

1.9 match 205 stars 5.83 score 111 scripts 1 dependents

ottlngr

LexisPlotR:Plot Lexis Diagrams for Demographic Purposes

Plots empty Lexis grids, adds lifelines and highlights certain areas of the grid, like cohorts and age groups.

Maintained by Philipp Ottolinger. Last updated 5 years ago.

2.1 match 25 stars 5.03 score 86 scripts

totajuliusd

topr:Create Custom Plots for Viewing Genetic Association Results

A collection of functions for visualizing,exploring and annotating genetic association results.Association results from multiple traits can be viewed simultaneously along with gene annotation, over the entire genome (Manhattan plot) or in the more detailed regional view.

Maintained by Thorhildur Juliusdottir. Last updated 6 months ago.

1.7 match 57 stars 6.38 score 30 scripts

yixuan

recosystem:Recommender System using Matrix Factorization

R wrapper of the 'libmf' library <https://www.csie.ntu.edu.tw/~cjlin/libmf/> for recommender system using matrix factorization. It is typically used to approximate an incomplete matrix using the product of two matrices in a latent space. Other common names for this task include "collaborative filtering", "matrix completion", "matrix recovery", etc. High performance multi-core parallel computing is supported in this package.

Maintained by Yixuan Qiu. Last updated 2 years ago.

matrix-factorization recommender-system cpp openmp

1.3 match 84 stars 7.97 score 101 scripts 6 dependents

loelschlaeger

fHMM:Fitting Hidden Markov Models to Financial Data

Fitting (hierarchical) hidden Markov models to financial data via maximum likelihood estimation. See Oelschläger, L. and Adam, T. "Detecting Bearish and Bullish Markets in Financial Time Series Using Hierarchical Hidden Markov Models" (2021, Statistical Modelling) <doi:10.1177/1471082X211034048> for a reference on the method. A user guide is provided by the accompanying software paper "fHMM: Hidden Markov Models for Financial Time Series in R", Oelschläger, L., Adam, T., and Michels, R. (2024, Journal of Statistical Software) <doi:10.18637/jss.v109.i09>.

Maintained by Lennart Oelschläger. Last updated 9 days ago.

finance hidden-markov-models cpp openmp

1.5 match 17 stars 7.04 score 5 scripts

bioc

made4:Multivariate analysis of microarray data using ADE4

Multivariate data analysis and graphical display of microarray data. Functions include for supervised dimension reduction (between group analysis) and joint dimension reduction of 2 datasets (coinertia analysis). It contains functions that require R package ade4.

Maintained by Aedin Culhane. Last updated 5 months ago.

clustering classification dimensionreduction principalcomponent transcriptomics multiplecomparison geneexpression sequencing microarray

1.7 match 6.11 score 107 scripts 2 dependents

bioc

ggkegg:Analyzing and visualizing KEGG information using the grammar of graphics

This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.

Maintained by Noriaki Sato. Last updated 2 months ago.

pathways dataimport kegg ggplot2 ggraph pathway tidygraph visualization

1.3 match 225 stars 8.08 score 30 scripts 1 dependents

nrcan

PlotFTIR:Plot FTIR Spectra

The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions. L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.

Maintained by Philip Bulsink. Last updated 13 hours ago.

chemometrics datavis ftir

2.0 match 5.02 score 5 scripts

glottospace

glottospace:Language Mapping and Geospatial Analysis of Linguistic and Cultural Data

Streamlined workflows for geolinguistic analysis, including: accessing global linguistic and cultural databases, data import, data entry, data cleaning, data exploration, mapping, visualization and export.

Maintained by Rui Dong. Last updated 4 months ago.

1.8 match 23 stars 5.54 score 6 scripts

gorelab

waves:Vis-NIR Spectral Analysis Wrapper

Originally designed application in the context of resource-limited plant research and breeding programs, 'waves' provides an open-source solution to spectral data processing and model development by bringing useful packages together into a streamlined pipeline. This package is wrapper for functions related to the analysis of point visible and near-infrared reflectance measurements. It includes visualization, filtering, aggregation, preprocessing, cross-validation set formation, model training, and prediction functions to enable open-source association of spectral and reference data. This package is documented in a peer-reviewed manuscript in the Plant Phenome Journal <doi:10.1002/ppj2.20012>. Specialized cross-validation schemes are described in detail in Jarquín et al. (2017) <doi:10.3835/plantgenome2016.12.0130>. Example data is from Ikeogu et al. (2017) <doi:10.1371/journal.pone.0188918>.

Maintained by Jenna Hershberger. Last updated 12 months ago.

1.7 match 6 stars 5.98 score 53 scripts

duncantl

CodeDepends:Analysis of R Code for Reproducible Research and Code Comprehension

Tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of functions. There are many facilities including the ability to summarize or get a high-level view of code, determining dependencies between variables, code improvement suggestions.

Maintained by Gabriel Becker. Last updated 1 years ago.

1.7 match 89 stars 5.87 score 70 scripts 1 dependents

ichcha-m

cophescan:Adaptation of the Coloc Method for PheWAS

A Bayesian method for Phenome-wide association studies (PheWAS) that identifies causal associations between genetic variants and traits, while simultaneously addressing confounding due to linkage disequilibrium. For details see Manipur et al (2023) <doi:10.1101/2023.06.29.546856>.

Maintained by Ichcha Manipur. Last updated 10 months ago.

cpp openmp

1.7 match 6 stars 5.76 score 24 scripts

dzmitrygb

Repliscope:Replication Timing Profiling using DNA Copy Number

Create, Plot and Compare Replication Timing Profiles. The method is described in Muller et al., (2014) <doi: 10.1093/nar/gkt878>.

Maintained by Dzmitry G Batrakou. Last updated 3 years ago.

3.1 match 3.13 score 27 scripts

mrjoh3

c3:'C3.js' Chart Library

Create interactive charts with the 'C3.js' <http://c3js.org/> charting library. All plot types in 'C3.js' are available and include line, bar, scatter, and mixed geometry plots. Plot annotations, labels and axis are highly adjustable. Interactive web based charts can be embedded in R Markdown documents or Shiny web applications.

Maintained by Matt Johnson. Last updated 4 years ago.

chart htmlwidget plots

1.5 match 39 stars 6.45 score 72 scripts

rjake

shinyobjects:Access Reactive Data Interactively

Troubleshooting reactive data in 'shiny' can be difficult. These functions will convert reactive data frames into functions and load all assigned objects into your local environment. If you create a dummy input object, as the function will suggest, you will be able to test your server and ui functions interactively.

Maintained by Jake Riley. Last updated 3 years ago.

1.8 match 22 stars 5.34 score 9 scripts

bioc

mosdef:MOSt frequently used and useful Differential Expression Functions

This package provides functionality to run a number of tasks in the differential expression analysis workflow. This encompasses the most widely used steps, from running various enrichment analysis tools with a unified interface to creating plots and beautifying table components linking to external websites and databases. This streamlines the generation of comprehensive analysis reports.

Maintained by Federico Marini. Last updated 3 months ago.

geneexpression software transcription transcriptomics differentialexpression visualization reportwriting genesetenrichment go

1.6 match 5.98 score 4 dependents

mundl

lfstat:Calculation of Low Flow Statistics for Daily Stream Flow Data

The "Manual on Low-flow Estimation and Prediction", published by the World Meteorological Organisation (WMO), gives a comprehensive summary on how to analyse stream flow data focusing on low-flows. This packages provides functions to compute the described statistics and produces plots similar to the ones in the manual.

Maintained by Tobias Gauster. Last updated 2 years ago.

1.9 match 11 stars 4.94 score 159 scripts

rkrug

plantuml:Create UML Graphs using PlantUML Syntax

Create UML graphs using the PlantUML language. These are either shown in a graphics device or saved as a file.

Maintained by Rainer M. Krug. Last updated 2 years ago.

1.7 match 78 stars 5.61 score 26 scripts

overton-group

eHDPrep:Quality Control and Semantic Enrichment of Datasets

A tool for the preparation and enrichment of health datasets for analysis (Toner et al. (2023) <doi:10.1093/gigascience/giad030>). Provides functionality for assessing data quality and for improving the reliability and machine interpretability of a dataset. 'eHDPrep' also enables semantic enrichment of a dataset where metavariables are discovered from the relationships between input variables determined from user-provided ontologies.

Maintained by Ian Overton. Last updated 2 years ago.

data-quality health-informatics semantic-enrichment

1.9 match 8 stars 4.90 score 10 scripts

bioc

smoppix:Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index

Test for univariate and bivariate spatial patterns in spatial omics data with single-molecule resolution. The tests implemented allow for analysis of nested designs and are automatically calibrated to different biological specimens. Tests for aggregation, colocalization, gradients and vicinity to cell edge or centroid are provided.

Maintained by Stijn Hawinkel. Last updated 1 months ago.

transcriptomics spatial singlecell cpp

1.8 match 1 stars 5.10 score 4 scripts

divadnojnarg

CaPO4Sim:A Virtual Patient Simulator in the Context of Calcium and Phosphate Homeostasis

Explore calcium (Ca) and phosphate (Pi) homeostasis with two novel 'Shiny' apps, building upon on a previously published mathematical model written in C, to ensure efficient computations. The underlying model is accessible here <https://pubmed.ncbi.nlm.nih.gov/28747359/)>. The first application explores the fundamentals of Ca-Pi homeostasis, while the second provides interactive case studies for in-depth exploration of the topic, thereby seeking to foster student engagement and an integrative understanding of Ca-Pi regulation.

Maintained by David Granjon. Last updated 2 months ago.

1.8 match 41 stars 4.94 score 14 scripts

mi2datalab

tidycharts:Generate Tidy Charts Inspired by 'IBCS'

There is a wide range of R packages created for data visualization, but still, there was no simple and easily accessible way to create clean and transparent charts - up to now. The 'tidycharts' package enables the user to generate charts compliant with International Business Communication Standards ('IBCS'). It means unified bar widths, colors, chart sizes, etc. Creating homogeneous reports has never been that easy! Additionally, users can apply semantic notation to indicate different data scenarios (plan, budget, forecast). What's more, it is possible to customize the charts by creating a personal color pallet with the possibility of switching to default options after the experiments. We wanted the package to be helpful in writing reports, so we also made joining charts in a one, clear image possible. All charts are generated in SVG format and can be shown in the 'RStudio' viewer pane or exported to HTML output of 'knitr'/'markdown'.

Maintained by Bartosz Sawicki. Last updated 3 years ago.

charts clean ibcs visualization

1.7 match 5 stars 5.23 score 17 scripts

openpharma

simaerep:Find Clinical Trial Sites Under-Reporting Adverse Events

Monitoring of Adverse Event (AE) reporting in clinical trials is important for patient safety. Sites that are under-reporting AEs can be detected using Bootstrap-based simulations that simulate overall AE reporting. Based on the simulation an AE under-reporting probability is assigned to each site in a given trial (Koneswarakantha 2021 <doi:10.1007/s40264-020-01011-5>).

Maintained by Bjoern Koneswarakantha. Last updated 2 months ago.

ae-reporting clinical-trials

1.7 match 22 stars 5.14 score 25 scripts

curious-joe

pell:Data About Historic Pell Grant Distribution in the US

Historic Pell grant data as provided by the US Department of Education. This package contains data about how much pell grant was awarded by which institution in which year. This data comes from the US Department of Education. Raw data can be downloaded from here: <https://www2.ed.gov/finaid/prof/resources/data/pell-institution.html>.

Maintained by Arafath Hossain. Last updated 2 years ago.

2.0 match 4.30 score 7 scripts

mkossmeier

metaviz:Forest Plots, Funnel Plots, and Visual Funnel Plot Inference for Meta-Analysis

A compilation of functions to create visually appealing and information-rich plots of meta-analytic data using 'ggplot2'. Currently allows to create forest plots, funnel plots, and many of their variants, such as rainforest plots, thick forest plots, additional evidence contour funnel plots, and sunset funnel plots. In addition, functionalities for visual inference with the funnel plot in the context of meta-analysis are provided.

Maintained by Michael Kossmeier. Last updated 5 years ago.

funnel-plots rainforest-plots

1.2 match 17 stars 7.32 score 135 scripts

bioc

ggmanh:Visualization Tool for GWAS Result

Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. The "ggmanh" package aims to keep the generation of these plots simple while maintaining customizability. Main functions include manhattan_plot, qqunif, and thinPoints.

Maintained by John Lee. Last updated 5 months ago.

visualization genomewideassociation genetics

2.0 match 4.26 score 23 scripts

bioc

Damsel:Damsel: an end to end analysis of DamID

Damsel provides an end to end analysis of DamID data. Damsel takes bam files from Dam-only control and fusion samples and counts the reads matching to each GATC region. edgeR is utilised to identify regions of enrichment in the fusion relative to the control. Enriched regions are combined into peaks, and are associated with nearby genes. Damsel allows for IGV style plots to be built as the results build, inspired by ggcoverage, and using the functionality and layering ability of ggplot2. Damsel also conducts gene ontology testing with bias correction through goseq, and future versions of Damsel will also incorporate motif enrichment analysis. Overall, Damsel is the first package allowing for an end to end analysis with visual capabilities. The goal of Damsel was to bring all the analysis into one place, and allow for exploratory analysis within R.

Maintained by Caitlin Page. Last updated 5 months ago.

differentialmethylation peakdetection geneprediction genesetenrichment

1.6 match 5.20 score 20 scripts

zachcp

phylocanvas:Interactive Phylogenetic Trees Using the 'Phylocanvas' JavaScript Library

Create and customize interactive phylogenetic trees using the 'phylocanvas' JavaScript library and the 'htmlwidgets' package. These trees can be used directly from the R console, from 'RStudio', in Shiny apps, and in R Markdown documents. See <http://phylocanvas.org/> for more information on the 'phylocanvas' library.

Maintained by zachary charlop-powers. Last updated 7 years ago.

htmlwidgets phylogeny

1.5 match 9 stars 5.45 score 31 scripts

bioc

CRISPRball:Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering

A Shiny application for visualization, exploration, comparison, and filtering of CRISPR screens analyzed with MAGeCK RRA or MLE. Features include interactive plots with on-click labeling, full customization of plot aesthetics, data upload and/or download, and much more. Quickly and easily explore your CRISPR screen results and generate publication-quality figures in seconds.

Maintained by Jared Andrews. Last updated 3 months ago.

software shinyapps crispr qualitycontrol visualization gui crispr-screen data-visualization interactive-visualizations mageck plotly screening shiny

1.3 match 9 stars 6.03 score 24 scripts

unhcr-dataviz

unhcrdown:UNHCR Branded Templates for R Markdown Documents

Create United Nations High Commissioner for Refugees (UNHCR) branded documents, presentations, and reports using R Markdown templates. This package provides customized formats that align with UNHCR's official brand guidelines for creating professional PDF reports, Word documents, PowerPoint presentations, and HTML outputs.

Maintained by Cédric Vidonne. Last updated 2 months ago.

pagedown rmarkdown rmarkdown-template xaringan

1.5 match 21 stars 5.32 score 1 scripts

mmedl94

lionfish:Interactive 'tourr' Using 'python'

Extends the functionality of the 'tourr' package by an interactive graphical user interface. The interactivity allows users to effortlessly refine their 'tourr' results by manual intervention, which allows for integration of expert knowledge and aids the interpretation of results. For more information on 'tourr' see Wickham et. al (2011) <doi:10.18637/jss.v040.i02> or <https://github.com/ggobi/tourr>.

Maintained by Matthias Medl. Last updated 8 days ago.

data-sience data-visualization dimensionality-reduction exploratory-data-analysis interactive interactive-visualizations tourr

1.3 match 1 stars 5.98 score

maliny12

sugarglider:Create Glyph-Maps of Spatiotemporal Data

Provides 'ggplot2' extensions to construct glyph-maps for visualizing seasonality in spatiotemporal data. See the Journal of Statistical Software reference: Zhang, H. S., Cook, D., Laa, U., Langrené, N., & Menéndez, P. (2024) <doi:10.18637/jss.v110.i07>. The manuscript for this package is currently under preparation and can be found on GitHub at <https://github.com/maliny12/paper-sugarglider>.

Maintained by Maliny Po. Last updated 3 months ago.

data-visualization

1.2 match 11 stars 6.68 score 7 scripts

bioc

clipper:Gene Set Analysis Exploiting Pathway Topology

Implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.

Maintained by Paolo Martini. Last updated 5 months ago.

1.7 match 4.48 score 19 scripts

ocbe-uio

DIscBIO:A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

An open, multi-algorithmic pipeline for easy, fast and efficient analysis of cellular sub-populations and the molecular signatures that characterize them. The pipeline consists of four successive steps: data pre-processing, cellular clustering with pseudo-temporal ordering, defining differential expressed genes and biomarker identification. More details on Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements extensions of the work published by Ghannoum et. al. (2019) <doi:10.1101/700989>.

Maintained by Waldir Leoncio. Last updated 1 years ago.

biomarker-discovery jupyter-notebook scrna-seq single-cell-analysis transcriptomics openjdk

1.8 match 12 stars 4.38 score 5 scripts

wolski

sigora:Signature Overrepresentation Analysis

Pathway Analysis is statistically linking observations on the molecular level to biological processes or pathways on the systems(i.e., organism, organ, tissue, cell) level. Traditionally, pathway analysis methods regard pathways as collections of single genes and treat all genes in a pathway as equally informative. However, this can lead to identifying spurious pathways as statistically significant since components are often shared amongst pathways. SIGORA seeks to avoid this pitfall by focusing on genes or gene pairs that are (as a combination) specific to a single pathway. In relying on such pathway gene-pair signatures (Pathway-GPS), SIGORA inherently uses the status of other genes in the experimental context to identify the most relevant pathways. The current version allows for pathway analysis of human and mouse datasets. In addition, it contains pre-computed Pathway-GPS data for pathways in the KEGG and Reactome pathway repositories and mechanisms for extracting GPS for user-supplied repositories.

Maintained by Witold Wolski. Last updated 3 years ago.

genesetenrichment go software pathways kegg

1.7 match 4.43 score 18 scripts 1 dependents

giocomai

castarter:Content Analysis Starter Toolkit

Consistent approaches for basic web scraping, text mining and word frequency analysis of textual datasets.

Maintained by Giorgio Comai. Last updated 1 days ago.

tada text-mining

1.6 match 3 stars 4.59 score 2 scripts

gastonmaurodiaz

rcaiman:CAnopy IMage ANalysis

Tools for pre-processing and processing canopy photographs with support for raw data reading. Works with images taken with both regular and fisheye lenses (all types). Includes algorithms specifically designed to mitigate errors caused by direct sunlight.

Maintained by Gastón Mauro Díaz. Last updated 8 hours ago.

2.0 match 1 stars 3.70 score 2 scripts

dipterix

shidashi:A Shiny Dashboard Template System

A template system based on 'AdminLTE3' (<https://adminlte.io/themes/v3/>) theme. Comes with default theme that can be easily customized. Developers can upload modified templates on 'Github', and users can easily download templates with 'RStudio' project wizard. The key features of the default template include light and dark theme switcher, resizing graphs, synchronizing inputs across sessions, new notification system, fancy progress bars, and card-like flip panels with back sides, as well as various of 'HTML' tool widgets.

Maintained by Zhengjia Wang. Last updated 1 years ago.

1.5 match 10 stars 4.72 score 35 scripts 1 dependents

fbertran

c060:Extended Inference for Lasso and Elastic-Net Regularized Cox and Generalized Linear Models

The c060 package provides additional functions to perform stability selection, model validation and parameter tuning for glmnet models.

Maintained by Frederic Bertrand. Last updated 2 years ago.

1.7 match 3 stars 4.35 score 37 scripts

talgalili

heatmaply:Interactive Cluster Heat Maps Using 'plotly' and 'ggplot2'

Create interactive cluster 'heatmaps' that can be saved as a stand- alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by 'dendrograms'. 'Heatmaps' are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' to 'heatmap.2' with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the 'heatmap'.

Maintained by Tal Galili. Last updated 9 months ago.

d3-heatmap dendextend dendrogram ggplot2 heatmap plotly

0.5 match 386 stars 14.21 score 2.0k scripts 45 dependents

bioc

Linnorm:Linear model and normality based normalization and transformation method (Linnorm)

Linnorm is an algorithm for normalizing and transforming RNA-seq, single cell RNA-seq, ChIP-seq count data or any large scale count data. It has been independently reviewed by Tian et al. on Nature Methods (https://doi.org/10.1038/s41592-019-0425-8). Linnorm can work with raw count, CPM, RPKM, FPKM and TPM.

Maintained by Shun Hang Yip. Last updated 5 months ago.

immunooncology sequencing chipseq rnaseq differentialexpression geneexpression genetics normalization software transcription batcheffect peakdetection clustering network singlecell cpp

1.1 match 6.26 score 61 scripts 5 dependents

ftwkoopmans

goat:Gene Set Analysis Using the Gene Set Ordinal Association Test

Perform gene set enrichment analyses using the Gene set Ordinal Association Test (GOAT) algorithm and visualize your results. Koopmans, F. (2024) <doi:10.1038/s42003-024-06454-5>.

Maintained by Frank Koopmans. Last updated 1 months ago.

bioinformatics geneset-enrichment geneset-enrichment-analysis cpp openmp

1.6 match 10 stars 4.40 score 8 scripts

teachinglab

tlShiny:Supplies essential functions to Teaching Lab dashboards

A bunch of random functions I use in developing dashboards Needs to vastly reduce the number of dependencies at the moment.

Maintained by Duncan Gates. Last updated 4 days ago.

2.3 match 3.04 score

sammo3182

drhutools:Political Science Academic Research Gears

Using these tools to simplify the research process of political science and other social sciences. The current version can create folder system for academic project in political science, calculate psychological trait scores, visualize experimental and spatial data, and set up color-blind palette, functions used in academic research of political psychology or political science in general.

Maintained by Yue Hu. Last updated 3 months ago.

1.5 match 2 stars 4.45 score 3 scripts

cran

parallelPlot:`htmlwidget` for a Parallel Coordinates Plot

Create a parallel coordinates plot, using `htmlwidgets` package and `d3.js`.

Maintained by David Chazalviel. Last updated 10 months ago.

2.3 match 3.00 score

yixuan

prettydoc:Creating Pretty Documents from R Markdown

Creating tiny yet beautiful documents and vignettes from R Markdown. The package provides the 'html_pretty' output format as an alternative to the 'html_document' and 'html_vignette' engines that convert R Markdown into HTML pages. Various themes and syntax highlight styles are supported.

Maintained by Yixuan Qiu. Last updated 4 years ago.

html markdown r-markdown

0.5 match 486 stars 12.90 score 550 scripts 8 dependents

elipousson

mapbaltimore:Make maps for Baltimore City with open data

This package provides data from the Baltimore City, the state of Maryland, and other sources, functions to access additional data, and function to create and modify simple maps of Baltimore neighborhoods using sf and ggplot2.

Maintained by Eli Pousson. Last updated 4 months ago.

baltimore rspatial

1.7 match 18 stars 3.88 score 14 scripts

bioc

CHRONOS:CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs.

Maintained by Panos Balomenos. Last updated 5 months ago.

systemsbiology graphandnetwork pathways kegg openjdk

1.7 match 3.86 score 12 scripts

cran

IPCAPS:Iterative Pruning to Capture Population Structure

An unsupervised clustering algorithm based on iterative pruning is for capturing population structure. This version supports ordinal data which can be applied directly to SNP data to identify fine-level population structure and it is built on the iterative pruning Principal Component Analysis ('ipPCA') algorithm as explained in Intarapanich et al. (2009) <doi:10.1186/1471-2105-10-382>. The 'IPCAPS' involves an iterative process using multiple splits based on multivariate Gaussian mixture modeling of principal components and 'Expectation-Maximization' clustering as explained in Lebret et al. (2015) <doi:10.18637/jss.v067.i06>. In each iteration, rough clusters and outliers are also identified using the function rubikclust() from the R package 'KRIS'.

Maintained by Kridsadakorn Chaichoompu. Last updated 4 years ago.

3.3 match 2.00 score

tntp

tntpr:Data Analysis Tools Customized for TNTP

An assortment of functions and templates customized to meet the needs of data analysts at the non-profit organization TNTP. Includes functions for branded colors and plots, credentials management, repository set-up, and other common analytic tasks.

Maintained by Dustin Pashouwer. Last updated 4 months ago.

1.2 match 7 stars 5.61 score 13 scripts

thermostats

RVA:RNAseq Visualization Automation

Automate downstream visualization & pathway analysis in RNAseq analysis. 'RVA' is a collection of functions that efficiently visualize RNAseq differential expression analysis result from summary statistics tables. It also utilize the Fisher's exact test to evaluate gene set or pathway enrichment in a convenient and efficient manner.

Maintained by Xingpeng Li. Last updated 3 years ago.

1.1 match 9 stars 5.65 score 6 scripts

kviswana

ezEDA:Task Oriented Interface for Exploratory Data Analysis

Enables users to create visualizations using functions based on the data analysis task rather than on plotting mechanics. It hides the details of the individual 'ggplot2' function calls and allows the user to focus on the end goal. Useful for quick preliminary explorations. Provides functions for common exploration patterns. Some of the ideas in this package are motivated by Fox (2015, ISBN:1938377052).

Maintained by Viswa Viswanathan. Last updated 4 years ago.

1.7 match 3.70 score 4 scripts

polinasuter

BiDAG:Bayesian Inference for Directed Acyclic Graphs

Implementation of a collection of MCMC methods for Bayesian structure learning of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient inference on larger DAGs, the space of DAGs is pruned according to the data. To filter the search space, the algorithm employs a hybrid approach, combining constraint-based learning with search and score. A reduced search space is initially defined on the basis of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with search and score. Search and score is then performed following two approaches: Order MCMC, or Partition MCMC. The BGe score is implemented for continuous data and the BDe score is implemented for binary data or categorical data. The algorithms may provide the maximum a posteriori (MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data. All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks. References: J. Kuipers, P. Suter, G. Moffa (2022) <doi:10.1080/10618600.2021.2020127>, N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>, J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>, M. Kalisch et al. (2012) <doi:10.18637/jss.v047.i11>, D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>, P. Suter, J. Kuipers, G. Moffa, N.Beerenwinkel (2023) <doi:10.18637/jss.v105.i09>.

Maintained by Polina Suter. Last updated 2 years ago.

cpp

1.9 match 4 stars 3.29 score 81 scripts 2 dependents

cran

scatterPlotMatrix:`htmlwidget` for a Scatter Plot Matrix

Create a scatter plot matrix, using `htmlwidgets` package and `d3.js`.

Maintained by David Chazalviel. Last updated 10 months ago.

2.3 match 2.70 score

bioc

TFEA.ChIP:Analyze Transcription Factor Enrichment

Package to analize transcription factor enrichment in a gene set using data from ChIP-Seq experiments.

Maintained by Laura Puente Santamaría. Last updated 5 months ago.

transcription generegulation genesetenrichment transcriptomics sequencing chipseq rnaseq immunooncology

1.8 match 3.45 score 14 scripts

mczek

mcStats:Visualize Results of Statistical Hypothesis Tests

Provides functionality to produce graphs of sampling distributions of test statistics from a variety of common statistical tests. With only a few keystrokes, the user can conduct a hypothesis test and visualize the test statistic and corresponding p-value through the shading of its sampling distribution. Initially created for statistics at Middlebury College.

Maintained by Michael Czekanski. Last updated 5 years ago.

2.0 match 3.00 score 1 scripts

gbasulto

ERDbuilder:Entity Relationship Diagrams Builder

Build entity relationship diagrams (ERD) to specify the nature of the relationship between tables in a database.

Maintained by Guillermo Basulto-Elias. Last updated 2 months ago.

1.2 match 2 stars 4.98 score 16 scripts