Showing 119 of total 119 results (show query)
bioc
motifStack:Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.
Maintained by Jianhong Ou. Last updated 3 months ago.
sequencematchingvisualizationsequencingmicroarrayalignmentchipchipchipseqmotifannotationdataimport
35.8 match 7.93 score 188 scripts 6 dependents
jpmonteagudo28
logos:Access to the Hebrew, Greek, and English Version of the Bible
Access to the Greek New Testament (27 books) and the Old Testament (39 books) and allow users to do textual analysis on the data. The New and Old Testament have been provided in their original languages, Greek and Hebrew, respectively. Additionally, the Revised American Standard Bible is also provided for users who'd rather use a word–for–word modern English translation.
Maintained by JP Monteagudo. Last updated 29 days ago.
50.0 match 3.70 scorebioc
universalmotif:Import, Modify, and Export Motifs with R
Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.
Maintained by Benjamin Jean-Marie Tremblay. Last updated 4 months ago.
motifannotationmotifdiscoverydataimportgeneregulationmotif-analysismotif-enrichment-analysissequence-logocpp
15.5 match 28 stars 11.04 score 342 scripts 12 dependents
parklab
Nozzle.R1:Nozzle Reports
The Nozzle package provides an API to generate HTML reports with dynamic user interface elements based on JavaScript and CSS (Cascading Style Sheets). Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big data sets. The package can be applied to any project where user-friendly reports need to be created.
Maintained by Nils Gehlenborg. Last updated 10 years ago.
gehlenborglabhtml-reportreproducible-research
29.7 match 68 stars 5.31 score 10 scripts 2 dependents
guangchuangyu
hexSticker:Create Hexagon Sticker in R
Helper functions for creating reproducible hexagon sticker purely in R.
Maintained by Guangchuang Yu. Last updated 2 months ago.
ggplot2hexagon-stickerlogostickersvisualization
11.0 match 769 stars 11.94 score 1.3k scripts 8 dependents
camdenk
mlbplotR:Create 'ggplot2' and 'gt' Visuals with Major League Baseball Logos
Tools to help visualize Major League Baseball analysis in 'ggplot2' and 'gt'. You provide team/player information and 'mlbplotR' will transform that information into team colors, logos, or player headshots for graphics.
Maintained by Camden Kay. Last updated 4 months ago.
baseballggplot2sportsdataverse
19.3 match 21 stars 5.97 score 111 scripts
omarwagih
ggseqlogo:A 'ggplot2' Extension for Drawing Publication-Ready Sequence Logos
The extensive range of functions provided by this package makes it possible to draw highly versatile sequence logos. Features include, but not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other plots 'ggplot2' plots.
Maintained by Omar Wagih. Last updated 5 months ago.
9.3 match 211 stars 11.48 score 786 scripts 13 dependentsbioc
seqLogo:Sequence logos for DNA sequence alignments
seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).
Maintained by Robert Ivanek. Last updated 5 months ago.
9.6 match 4 stars 10.57 score 304 scripts 29 dependents
yonicd
slickR:Create Interactive Carousels with the 'JavaScript' 'Slick' Library
Create and customize interactive carousels using the 'Slick' 'JavaScript' library and the 'htmlwidgets' package. The carousels can contain plots produced in R, images, 'iframes', videos and other 'htmlwidgets'. These carousels can be created directly from the R console, and viewed in the 'RStudio' internal viewer, in 'Shiny' apps and R Markdown documents.
Maintained by Jonathan Sidi. Last updated 1 years ago.
8.0 match 160 stars 9.37 score 199 scripts 1 dependents
adeverse
ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Maintained by Aurélie Siberchicot. Last updated 15 days ago.
4.5 match 39 stars 14.96 score 2.2k scripts 256 dependentsadeverse
adegraphics:An S4 Lattice-Based Package for the Representation of Multivariate Data
Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Maintained by Aurélie Siberchicot. Last updated 8 months ago.
6.0 match 9 stars 10.37 score 386 scripts 6 dependents
nflverse
nflplotR:NFL Logo Plots in 'ggplot2' and 'gt'
A set of functions to visualize National Football League analysis in 'ggplot2' plots and 'gt' tables.
Maintained by Sebastian Carl. Last updated 14 days ago.
nflnflfastrnflstatsnflversesports-analyticssportsanalytics
8.2 match 20 stars 7.20 score 316 scripts 1 dependents
ropensci
magick:Advanced Graphics and Image-Processing in R
Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.
Maintained by Jeroen Ooms. Last updated 23 days ago.
image-manipulationimage-processingimagemagickcpp
3.3 match 468 stars 17.31 score 9.0k scripts 256 dependents
mihaiconstantin
parabar:Progress Bar for Parallel Tasks
A simple interface in the form of R6 classes for executing tasks in parallel, tracking their progress, and displaying accurate progress bars.
Maintained by Mihai Constantin. Last updated 3 months ago.
parallel-computingprogress-bar
7.6 match 20 stars 7.56 score 20 scripts 5 dependents
trevorld
ggpattern:'ggplot2' Pattern Geoms
Provides 'ggplot2' geoms filled with various patterns. Includes a patterned version of every 'ggplot2' geom that has a region that can be filled with a pattern. Provides a suite of 'ggplot2' aesthetics and scales for controlling pattern appearances. Supports over a dozen builtin patterns (every pattern implemented by 'gridpattern') as well as allowing custom user-defined patterns.
Maintained by Trevor L. Davis. Last updated 2 months ago.
4.6 match 368 stars 12.33 score 1.7k scripts 3 dependents
massimoaria
bibliometrix:Comprehensive Science Mapping Analysis
Tool for quantitative research in scientometrics and bibliometrics. It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>. 'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS', 'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions' (<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>), and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Maintained by Massimo Aria. Last updated 5 hours ago.
bibliometric-analysisbibliometricscitationcitation-networkcitationsco-authorsco-occurenceco-word-analysiscorrespondence-analysiscouplingisi-webjournalmanuscriptquantitative-analysisscholarssciencescience-mappingscientificscientometricsscopus
4.5 match 545 stars 12.54 score 518 scripts 2 dependentsbioc
monaLisa:Binned Motif Enrichment Analysis and Visualization
Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided.
Maintained by Michael Stadler. Last updated 2 months ago.
motifannotationvisualizationfeatureextractionepigenetics
6.5 match 40 stars 8.06 score 53 scripts
jgraux
DepLogo:Dependency Logo
Plots dependency logos from a set of aligned input sequences.
Maintained by Jan Grau. Last updated 1 years ago.
18.5 match 1 stars 2.41 score 26 scripts
luisdva
hexsession:Create a tile of logos for loaded packages
Creates a responsive HTML file with tiled hex logos for all loaded packages in a session, which can be saved as a static screenshot in png format.
Maintained by Luis D. Verde Arregoitia. Last updated 1 months ago.
9.4 match 35 stars 4.20 score 4 scriptsnflverse
nflfastR:Functions to Efficiently Access NFL Play by Play Data
A set of functions to access National Football League play-by-play data from <https://www.nfl.com/>.
Maintained by Ben Baldwin. Last updated 2 months ago.
american-footballfootball-datanflnflstatsnflversesports-analytics
3.5 match 442 stars 10.40 score 596 scripts 3 dependents
tidyverse
tidyverse:Easily Install and Load the 'Tidyverse'
The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step. Learn more about the 'tidyverse' at <https://www.tidyverse.org>.
Maintained by Hadley Wickham. Last updated 5 months ago.
1.8 match 1.7k stars 20.26 score 664k scripts 125 dependents
r-lib
usethis:Automate Package and Project Setup
Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.
Maintained by Jennifer Bryan. Last updated 14 days ago.
2.0 match 869 stars 17.54 score 5.6k scripts 336 dependentsr-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 17 hours ago.
1.9 match 734 stars 18.46 score 588 scripts 162 dependents
r-tmap
tmap:Thematic Maps
Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Maintained by Martijn Tennekes. Last updated 7 days ago.
choropleth-mapsmapsspatialthematic-mapsvisualisation
2.0 match 880 stars 16.73 score 13k scripts 24 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.
3.8 match 22 stars 8.80 score 280 scripts 1 dependents
hughjonesd
huxtable:Easily Create and Style Tables for LaTeX, HTML and Other Formats
Creates styled tables for data presentation. Export to HTML, LaTeX, RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate borders, size, position, captions, colours, text styles and number formatting. Table cells can span multiple rows and/or columns. Includes a 'huxreg' function for creation of regression tables, and 'quick_*' one-liners to print data to a new document.
Maintained by David Hugh-Jones. Last updated 15 days ago.
htmlhuxtablelatexmicrosoft-wordpowerpointreproducible-researchtables
2.3 match 323 stars 13.93 score 1.9k scripts 16 dependents
leonawicz
rtrek:Data Analysis Relating to Star Trek
Provides datasets related to the Star Trek fictional universe and functions for working with the data. The package also provides access to real world datasets based on the televised series and other related licensed media productions. It interfaces with the Star Trek API (STAPI) (<http://stapi.co/>), Memory Alpha (<https://memory-alpha.fandom.com/wiki/Portal:Main>), and Memory Beta (<https://memory-beta.fandom.com/wiki/Main_Page>) to retrieve data, metadata and other information relating to Star Trek. It also contains several local datasets covering a variety of topics. The package also provides functions for working with data from other Star Trek-related R data packages containing larger datasets not stored in 'rtrek'.
Maintained by Matthew Leonawicz. Last updated 6 months ago.
5.8 match 54 stars 5.42 score 49 scripts
theeliteanalyst
Riex:IEX Stocks and Market Data
Retrieves efficiently and reliably Investors Exchange ('IEX') stock and market data using 'IEX Cloud API'. The platform is offered by Investors Exchange Group (IEX Group). Main goal is to leverage 'R' capabilities including existing packages to effectively provide financial and statistical analysis as well as visualization in support of fact-based decisions. In addition, continuously improve and enhance 'Riex' by applying best practices and being in tune with users' feedback and requirements. Please, make sure to review and acknowledge Investors Exchange Group (IEX Group) terms and conditions before using 'Riex' (<https://iexcloud.io/terms/>).
Maintained by Myriam Ibrahim. Last updated 4 years ago.
financefinancial-analysisfinancial-dataiexiex-apiiexcloud
6.5 match 9 stars 4.69 score 11 scriptsbioc
atSNP:Affinity test for identifying regulatory SNPs
atSNP performs affinity tests of motif matches with the SNP or the reference genomes and SNP-led changes in motif matches.
Maintained by Sunyoung Shin. Last updated 5 months ago.
softwarechipseqgenomeannotationmotifannotationvisualizationcpp
4.8 match 1 stars 5.73 score 36 scriptsbioc
seqArchR:Identify Different Architectures of Sequence Elements
seqArchR enables unsupervised discovery of _de novo_ clusters with characteristic sequence architectures characterized by position-specific motifs or composition of stretches of nucleotides, e.g., CG-richness. seqArchR does _not_ require any specifications w.r.t. the number of clusters, the length of any individual motifs, or the distance between motifs if and when they occur in pairs/groups; it directly detects them from the data. seqArchR uses non-negative matrix factorization (NMF) as its backbone, and employs a chunking-based iterative procedure that enables processing of large sequence collections efficiently. Wrapper functions are provided for visualizing cluster architectures as sequence logos.
Maintained by Sarvesh Nikumbh. Last updated 5 months ago.
motifdiscoverygeneregulationmathematicalbiologysystemsbiologytranscriptomicsgeneticsclusteringdimensionreductionfeatureextractiondnaseqnmfnonnegative-matrix-factorizationpromoter-sequence-architecturesscikit-learnsequence-analysissequence-architecturesunsupervised-machine-learning
5.8 match 1 stars 4.48 score 9 scripts 1 dependentsbioc
TFBSTools:Software Package for Transcription Factor Binding Site (TFBS) Analysis
TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.
Maintained by Ge Tan. Last updated 7 days ago.
motifannotationgeneregulationmotifdiscoverytranscriptionalignment
2.0 match 28 stars 12.36 score 1.1k scripts 18 dependents
sstoeckl
crypto2:Download Crypto Currency Data from 'CoinMarketCap' without 'API'
Retrieves crypto currency information and historical prices as well as information on the exchanges they are listed on. Historical data contains daily open, high, low and close values for all crypto currencies. All data is scraped from <https://coinmarketcap.com> via their 'web-api'.
Maintained by Sebastian Stoeckl. Last updated 9 days ago.
3.2 match 56 stars 7.33 score 60 scripts 1 dependents
gadenbuie
xaringanExtra:Extras and Extensions for 'xaringan' Slides
Extras and extensions for 'xaringan' slides. Navigate your slides with tile view. Make your slides editable, live! Announce slide changes with subtle tones. Animate slide transitions with 'animate.css'. Add tabbed panels to slides with 'panelset'. Use the 'Tachyons CSS' utility toolkit for rapid slide development. Scribble on your slides. Add a copy button to your code chunks with 'clipboard'. Add a logo or top or bottom banner to every slide. Broadcast slides to stay in sync with remote viewers. Include yourself in your slides with 'webcam'. Plus a whole lot more!
Maintained by Garrick Aden-Buie. Last updated 10 months ago.
remarkjsrmarkdownslidestabsxaringanxaringan-slides
2.8 match 450 stars 8.41 score 1.9k scripts 1 dependents
alexchristensen
NetworkToolbox:Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis
Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershgoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.
Maintained by Alexander Christensen. Last updated 2 years ago.
3.3 match 23 stars 6.99 score 101 scripts 4 dependents
lz100
spsComps:'systemPipeShiny' UI and Server Components
The systemPipeShiny (SPS) framework comes with many UI and server components. However, installing the whole framework is heavy and takes some time. If you would like to use UI and server components from SPS in your own Shiny apps, do not hesitate to try this package.
Maintained by Le Zhang. Last updated 1 years ago.
3.4 match 31 stars 6.56 score 65 scripts 4 dependents
dreamrs
shinybusy:Busy Indicators and Notifications for 'Shiny' Applications
Add indicators (spinner, progress bar, gif) in your 'shiny' applications to show the user that the server is busy. And other tools to let your users know something is happening (send notifications, reports, ...).
Maintained by Victor Perrier. Last updated 6 months ago.
1.9 match 142 stars 11.70 score 772 scripts 39 dependentsnflverse
nflreadr:Download 'nflverse' Data
A minimal package for downloading data from 'GitHub' repositories of the 'nflverse' project.
Maintained by Tan Ho. Last updated 4 months ago.
nflnflfastrnflversesports-data
1.8 match 66 stars 12.46 score 476 scripts 10 dependents
tslumley
rmeta:Meta-Analysis
Functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. Draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.
Maintained by Thomas Lumley. Last updated 7 years ago.
3.8 match 1 stars 5.62 score 219 scripts 20 dependents
lcbc-uio
lcbcr:LCBC brand package
Functions and setups with brand styling and lab general setups.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
6.9 match 3.00 score 2 scripts
ropensci
weatherOz:An API Client for Australian Weather and Climate Data Resources
Provides automated downloading, parsing and formatting of weather data for Australia through API endpoints provided by the Department of Primary Industries and Regional Development ('DPIRD') of Western Australia and by the Science and Technology Division of the Queensland Government's Department of Environment and Science ('DES'). As well as the Bureau of Meteorology ('BOM') of the Australian government precis and coastal forecasts, and downloading and importing radar and satellite imagery files. 'DPIRD' weather data are accessed through public 'APIs' provided by 'DPIRD', <https://www.agric.wa.gov.au/weather-api-20>, providing access to weather station data from the 'DPIRD' weather station network. Australia-wide weather data are based on data from the Australian Bureau of Meteorology ('BOM') data and accessed through 'SILO' (Scientific Information for Land Owners) Jeffrey et al. (2001) <doi:10.1016/S1364-8152(01)00008-1>. 'DPIRD' data are made available under a Creative Commons Attribution 3.0 Licence (CC BY 3.0 AU) license <https://creativecommons.org/licenses/by/3.0/au/deed.en>. SILO data are released under a Creative Commons Attribution 4.0 International licence (CC BY 4.0) <https://creativecommons.org/licenses/by/4.0/>. 'BOM' data are (c) Australian Government Bureau of Meteorology and released under a Creative Commons (CC) Attribution 3.0 licence or Public Access Licence ('PAL') as appropriate, see <http://www.bom.gov.au/other/copyright.shtml> for further details.
Maintained by Rodrigo Pires. Last updated 23 days ago.
dpirdbommeteorological-dataweather-forecastaustraliaweatherweather-datameteorologywestern-australiaaustralia-bureau-of-meteorologywestern-australia-agricultureaustralia-agricultureaustralia-climateaustralia-weatherapi-clientclimatedatarainfallweather-api
2.3 match 32 stars 8.54 score 40 scripts
dobrowski
MCOE:Creates New Folders and Loads Standard Practices for Monterey County Office of Education
Basic Setup for Projects in R for Monterey County Office of Education. It contains functions often used in the analysis of education data in the county office including seeing if an item is not in a list, rounding in the manner the general public expects, including logos for districts, switching between district names and their county-district-school codes, accessing the local 'SQL' table and making thematically consistent graphs.
Maintained by David Dobrowski. Last updated 1 years ago.
6.1 match 1 stars 3.11 score 26 scriptsbioc
seqArchRplus:Downstream analyses of promoter sequence architectures and HTML report generation
seqArchRplus facilitates downstream analyses of promoter sequence architectures/clusters identified by seqArchR (or any other tool/method). With additional available information such as the TPM values and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus can order the input promoter clusters by their shape (IQWs), and write the cluster information as browser/IGV track files. Provided visualizations are of two kind: per sample/stage and per cluster visualizations. Those of the first kind include: plot panels for each sample showing per cluster shape, TPM and other score distributions, sequence logos, and peak annotations. The second include per cluster chromosome-wise and strand distributions, motif occurrence heatmaps and GO term enrichments. Additionally, seqArchRplus can also generate HTML reports for easy viewing and comparison of promoter architectures between samples/stages.
Maintained by Sarvesh Nikumbh. Last updated 5 months ago.
annotationvisualizationreportwritinggomotifannotationclustering
4.6 match 1 stars 4.00 score 2 scripts
hypertidy
ximage:Draw Images of Raster Data and Related Adornments
Draw images easily and as if doing that was considered desirable or even essential to be able to do. Set up a plot with an image, specify where that image should be placed. Image plot by default reflects the index of the image data itself, or can be specified in simple extent terms 'xmin,xmax,ymin,ymax'. Numeric matrices, integer arrays, byte arrays, character arrays, and native rasters are (or will be) supported. A little bit like 'image()' and 'rasterImage()' from the 'graphics' package but with the good features celebrated and made easier to use.
Maintained by Michael D. Sumner. Last updated 7 months ago.
5.6 match 8 stars 3.25 score 22 scripts
ss3sim
ss3sim:Fisheries Stock Assessment Simulation Testing with Stock Synthesis
A framework for fisheries stock assessment simulation testing with Stock Synthesis (SS3) as described in Anderson et al. (2014) <doi:10.1371/journal.pone.0092725>.
Maintained by Kelli F. Johnson. Last updated 5 months ago.
fisheriessimulationstock-synthesis
2.0 match 39 stars 8.89 score 149 scripts
laresbernardo
lares:Analytics & Machine Learning Sidekick
Auxiliary package for better/faster analytics, visualization, data mining, and machine learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling, Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust results, without the need of repetitive coding or advanced R programming skills.
Maintained by Bernardo Lares. Last updated 27 days ago.
analyticsapiautomationautomldata-sciencedescriptive-statisticsh2omachine-learningmarketingmmmpredictive-modelingpuzzlerlanguagerobynvisualization
1.8 match 233 stars 9.84 score 185 scripts 1 dependents
wadpac
GGIR:Raw Accelerometer Data Analysis
A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.
Maintained by Vincent T van Hees. Last updated 5 days ago.
accelerometeractivity-recognitioncircadian-rhythmmovement-sensorsleep
1.3 match 109 stars 13.20 score 342 scripts 3 dependents
riatelab
mapsf:Thematic Cartography
Create and integrate thematic maps in your workflow. This package helps to design various cartographic representations such as proportional symbols, choropleth or typology maps. It also offers several functions to display layout elements that improve the graphic presentation of maps (e.g. scale bar, north arrow, title, labels). 'mapsf' maps 'sf' objects on 'base' graphics.
Maintained by Timothée Giraud. Last updated 1 days ago.
cartographymapspatialspatial-analysis
1.5 match 229 stars 11.32 score 414 scripts 12 dependents
coatless-rpkg
surreal:Create Datasets with Hidden Images in Residual Plots
Implements the "Residual (Sur)Realism" algorithm described by Stefanski (2007) <doi:10.1198/000313007X190079> to generate datasets that reveal hidden images or messages in their residual plots. It offers both predefined datasets and tools to embed custom text or images into residual structures. Allowing users to create intriguing visual demonstrations for teaching model diagnostics.
Maintained by James Joseph Balamuta. Last updated 6 months ago.
diagnostic-plotsresidual-analysisresiduals
3.8 match 15 stars 4.57 score 4 scriptsbioc
dagLogo:dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory
Visualize significant conserved amino acid sequence pattern in groups based on probability theory.
Maintained by Jianhong Ou. Last updated 3 months ago.
3.8 match 4.48 score 9 scripts
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 25 days ago.
bioinformaticsgeneset-enrichmentgeneset-enrichment-analysiscppopenmp
3.8 match 10 stars 4.40 score 8 scripts
nlmixr2
nlmixr2est:Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines
Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Maintained by Matthew Fidler. Last updated 2 days ago.
2.0 match 9 stars 8.33 score 26 scripts 9 dependents
immunomind
immunarch:Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
Maintained by Vadim I. Nazarov. Last updated 1 years ago.
airr-analysisb-cell-receptorbcrbcr-repertoirebioinformaticsigig-repertoireimmune-repertoireimmune-repertoire-analysisimmune-repertoire-dataimmunoglobulinimmunoinformaticsimmunologyrep-seqrepertoire-analysissingle-cellsingle-cell-analysist-cell-receptortcrtcr-repertoirecpp
1.8 match 315 stars 9.49 score 203 scriptsbioc
RcisTarget:RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions
RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).
Maintained by Gert Hulselmans. Last updated 5 months ago.
generegulationmotifannotationtranscriptomicstranscriptiongenesetenrichmentgenetarget
1.8 match 37 stars 9.47 score 191 scriptsbioc
scShapes:A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data
We present a novel statistical framework for identifying differential distributions in single-cell RNA-sequencing (scRNA-seq) data between treatment conditions by modeling gene expression read counts using generalized linear models (GLMs). We model each gene independently under each treatment condition using error distributions Poisson (P), Negative Binomial (NB), Zero-inflated Poisson (ZIP) and Zero-inflated Negative Binomial (ZINB) with log link function and model based normalization for differences in sequencing depth. Since all four distributions considered in our framework belong to the same family of distributions, we first perform a Kolmogorov-Smirnov (KS) test to select genes belonging to the family of ZINB distributions. Genes passing the KS test will be then modeled using GLMs. Model selection is done by calculating the Bayesian Information Criterion (BIC) and likelihood ratio test (LRT) statistic.
Maintained by Malindrie Dharmaratne. Last updated 5 months ago.
rnaseqsinglecellmultiplecomparisongeneexpression
3.3 match 8 stars 4.90 score 6 scripts
fabnavarro
gasper:Graph Signal Processing
Provides the standard operations for signal processing on graphs: graph Fourier transform, spectral graph wavelet transform, visualization tools. It also implements a data driven method for graph signal denoising/regression, for details see De Loynes, Navarro, Olivier (2019) <arxiv:1906.01882>. The package also provides an interface to the SuiteSparse Matrix Collection, <https://sparse.tamu.edu/>, a large and widely used set of sparse matrix benchmarks collected from a wide range of applications.
Maintained by Fabien Navarro. Last updated 7 months ago.
data-sciencegraphgraph-signal-processinggraph-waveletmachine-learningspectral-graph-theorystatisticssuitesparsewavelet-transformopenblascpp
4.0 match 8 stars 4.03 score 27 scripts
tabima
effectR:Predicts Oomycete Effectors
Predicts cytoplasmic effector proteins using genomic data by searching for motifs of interest using regular expression searches and hidden Markov models (HMM) based in Haas et al. (2009) <doi:10.1038/nature08358>.
Maintained by Javier Tabima. Last updated 6 years ago.
3.4 match 1 stars 4.59 score 13 scriptsbioc
abseqR:Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. abseqR empowers the users of abseqPy (https://github.com/malhamdoosh/abseqPy) with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output.
Maintained by JiaHong Fong. Last updated 5 months ago.
sequencingvisualizationreportwritingqualitycontrolmultiplecomparison
3.8 match 4.00 score 3 scripts
flavjack
huito:Reproducible and Flexible Label Design
An open-source R package to deploys reproducible and flexible labels using layers. The 'huito' package is part of the 'inkaverse' project for developing different procedures and tools used in plant science and experimental designs. Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Maintained by Flavio Lozano-Isla. Last updated 7 months ago.
3.0 match 1 stars 4.79 score 31 scripts
thierryo
qrcode:Generate QRcodes with R
Create static QR codes in R. The content of the QR code is exactly what the user defines. We don't add a redirect URL, making it impossible for us to track the usage of the QR code. This allows to generate fast, free to use and privacy friendly QR codes.
Maintained by Thierry Onkelinx. Last updated 6 months ago.
qrcodeqrcode-generatorr-project
1.9 match 44 stars 7.56 score 456 scripts 7 dependents
hypertidy
vapour:Access to the 'Geospatial Data Abstraction Library' ('GDAL')
Provides low-level access to 'GDAL' functionality. 'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats that presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable developing further tools.
Maintained by Michael Sumner. Last updated 9 months ago.
1.5 match 86 stars 9.31 score 63 scripts 5 dependentstrevorld
affiner:A Finer Way to Render 3D Illustrated Objects in 'grid' Using Affine Transformations
Dilate, permute, project, reflect, rotate, shear, and translate 2D and 3D points. Supports parallel projections including oblique projections such as the cabinet projection as well as axonometric projections such as the isometric projection. Use 'grid's "affine transformation" feature to render illustrated flat surfaces.
Maintained by Trevor L. Davis. Last updated 3 months ago.
2.0 match 9 stars 6.91 score 1 scripts 5 dependentsbioc
CAGEr:Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.
Maintained by Charles Plessy. Last updated 5 months ago.
preprocessingsequencingnormalizationfunctionalgenomicstranscriptiongeneexpressionclusteringvisualization
2.3 match 6.12 score 73 scripts
inbo
checklist:A Thorough and Strict Set of Checks for R Packages and Source Code
An opinionated set of rules for R packages and R source code projects.
Maintained by Thierry Onkelinx. Last updated 29 days ago.
checklistcontinuous-integrationcontinuous-testingquality-assurance
1.9 match 19 stars 7.24 score 21 scripts 2 dependents
djnavarro
rainbowr:Make LGBT Hexes and Flags
Generates a variety of LGBT flags (e.g., rainbow, transgender) overlaid with the R logo, using the magick package. Also generates hex stickers based on LGBT flags and tilings thereof.
Maintained by Danielle Navarro. Last updated 5 years ago.
4.0 match 23 stars 3.40 score 22 scriptsbioc
DiffLogo:DiffLogo: A comparative visualisation of biooligomer motifs
DiffLogo is an easy-to-use tool to visualize motif differences.
Maintained by Hendrik Treutler. Last updated 5 months ago.
softwaresequencematchingmultiplecomparisonmotifannotationvisualizationalignment
2.0 match 8 stars 6.66 score 27 scripts
bczernecki
thunder:Computation and Visualisation of Atmospheric Convective Parameters
Allow to compute and visualise convective parameters commonly used in the operational prediction of severe convective storms. Core algorithm is based on a highly optimized 'C++' code linked into 'R' via 'Rcpp'. Highly efficient engine allows to derive thermodynamic and kinematic parameters from large numerical datasets such as reanalyses or operational Numerical Weather Prediction models in a reasonable amount of time. Package has been developed since 2017 by research meteorologists specializing in severe thunderstorms. The most relevant methods used in the package based on the following publications Stipanuk (1973) <https://apps.dtic.mil/sti/pdfs/AD0769739.pdf>, McCann et al. (1994) <doi:10.1175/1520-0434(1994)009%3C0532:WNIFFM%3E2.0.CO;2>, Bunkers et al. (2000) <doi:10.1175/1520-0434(2000)015%3C0061:PSMUAN%3E2.0.CO;2>, Corfidi et al. (2003) <doi:10.1175/1520-0434(2003)018%3C0997:CPAMPF%3E2.0.CO;2>, Showalter (1953) <doi:10.1175/1520-0477-34.6.250>, Coffer et al. (2019) <doi:10.1175/WAF-D-19-0115.1>, Gropp and Davenport (2019) <doi:10.1175/WAF-D-17-0150.1>, Czernecki et al. (2019) <doi:10.1016/j.atmosres.2019.05.010>, Taszarek et al. (2020) <doi:10.1175/JCLI-D-20-0346.1>, Sherburn and Parker (2014) <doi:10.1175/WAF-D-13-00041.1>, Romanic et al. (2022) <doi:10.1016/j.wace.2022.100474>.
Maintained by Bartosz Czernecki. Last updated 12 months ago.
capecinconvective-parametersdownload-soundinghodographrawinsondesevere-weatherthundertornadocpp
2.1 match 45 stars 6.31 score 7 scriptsbioc
EGSEA:Ensemble of Gene Set Enrichment Analyses
This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. EGSEA algorithm utilizes the analysis results of twelve prominent GSE algorithms in the literature to calculate collective significance scores for each gene set.
Maintained by Monther Alhamdoosh. Last updated 5 months ago.
immunooncologydifferentialexpressiongogeneexpressiongenesetenrichmentgeneticsmicroarraymultiplecomparisononechannelpathwaysrnaseqsequencingsoftwaresystemsbiologytwochannelmetabolomicsproteomicskegggraphandnetworkgenesignalinggenetargetnetworkenrichmentnetworkclassification
2.3 match 5.81 score 64 scriptsbioc
tripr:T-cell Receptor/Immunoglobulin Profiler (TRIP)
TRIP is a software framework that provides analytics services on antigen receptor (B cell receptor immunoglobulin, BcR IG | T cell receptor, TR) gene sequence data. It is a web application written in R Shiny. It takes as input the output files of the IMGT/HighV-Quest tool. Users can select to analyze the data from each of the input samples separately, or the combined data files from all samples and visualize the results accordingly.
Maintained by Nikolaos Pechlivanis. Last updated 5 months ago.
batcheffectmultiplecomparisongeneexpressionimmunooncologytargetedresequencingbioconductorclonotype
2.2 match 2 stars 5.48 score 4 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 7 months ago.
brandingcolorcolor-palettescolor-schemescorporate-designuniversity-colorsvisual-identity
1.8 match 9 stars 6.58 score 10 scripts
asa12138
MetaNet:Network Analysis for Omics Data
Comprehensive network analysis package. Calculate correlation network fastly, accelerate lots of analysis by parallel computing. Support for multi-omics data, search sub-nets fluently. Handle bigger data, more than 10,000 nodes in each omics. Offer various layout method for multi-omics network and some interfaces to other software ('Gephi', 'Cytoscape', 'ggplot2'), easy to visualize. Provide comprehensive topology indexes calculation, including ecological network stability.
Maintained by Chen Peng. Last updated 10 hours ago.
dataimportnetwork analysisomicssoftwarevisualization
2.0 match 13 stars 5.59 score 9 scripts
matt-dray
pixeltrix:A Simple Interactive Pixel Art Editor
A very simple 'pixel art' tool that lets you click squares interactively in a plot window and returns your final image as a matrix. Provide multiple frames to create an animated gif.
Maintained by Matt Dray. Last updated 10 months ago.
3.4 match 23 stars 3.17 score 13 scripts
oobianom
nextGenShinyApps:Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts and style sheets are based on 'jQuery' <https://jquery.com/> and 'Bootstrap' <https://getbootstrap.com/>.
Maintained by Obinna Obianom. Last updated 8 months ago.
1.7 match 10 stars 5.95 score 59 scripts 1 dependents
johannesfriedrich
qoi:Read and Write QOI Images
The new QOI file format offers a very simple but efficient image compression algorithm. This package provides an easy and simple way to read, write and display bitmap images stored in the QOI (Quite Ok Image) format. It can read and write both files and in-memory raw vectors.
Maintained by Johannes Friedrich. Last updated 2 months ago.
3.3 match 3 stars 2.95 score 3 scripts
loelschlaeger
oeli:Utilities for Developing Data Science Software
Some general helper functions that I (and maybe others) find useful when developing data science software.
Maintained by Lennart Oelschläger. Last updated 4 months ago.
1.8 match 2 stars 5.42 score 1 scripts 4 dependents
dillonhammill
DataEditR:An Interactive Editor for Viewing, Entering, Filtering & Editing Data
An interactive editor built on 'rhandsontable' to allow the interactive viewing, entering, filtering and editing of data in R <https://dillonhammill.github.io/DataEditR/>.
Maintained by Dillon Hammill. Last updated 2 years ago.
1.3 match 385 stars 7.79 score 106 scripts 1 dependents
bupaverse
bupaverse:Easily Install and Load the 'bupaverse'
The 'bupaverse' is an open-source, integrated suite of R-packages for handling and analysing business process data, developed by the Business Informatics research group at Hasselt University, Belgium. Profoundly inspired by the 'tidyverse' package, the 'bupaverse' package is designed to facilitate the installation and loading of multiple 'bupaverse' packages in a single step. Learn more about 'bupaverse' at the <https://bupar.net> homepage.
Maintained by Gert Janssenswillen. Last updated 2 years ago.
2.3 match 2 stars 4.32 score 21 scripts
ropengov
rogtemplate:'pkgdown' Template for 'rOpenGov' Packages
This is a private template for use by core rOpenGov packages. Please don’t use for your own code.
Maintained by Diego Hernangómez. Last updated 23 hours ago.
ropengovtemplategithub-actionspkgdownpkgdown-template
1.9 match 2 stars 5.16 score 3 scripts
grantmcdermott
parttree:Visualize Simple 2-D Decision Tree Partitions
Visualize the partitions of simple decision trees, involving one or two predictors, on the scale of the original data. Provides an intuitive alternative to traditional tree diagrams, by visualizing how a decision tree divides the predictor space in a simple 2D plot alongside the original data. The 'parttree' package supports both classification and regression trees from 'rpart' and 'partykit', as well as trees produced by popular frontend systems like 'tidymodels' and 'mlr3'. Visualization methods are provided for both base R graphics and 'ggplot2'.
Maintained by Grant McDermott. Last updated 2 months ago.
1.3 match 98 stars 7.73 score 91 scriptslcbc-uio
noasr:NOAS convenience functions
Functions created to work well with LCBC's Nephew of All Spreadsheet data.
Maintained by Athanasia Mo Mowinckel. Last updated 4 years ago.
3.2 match 3.00 score 4 scripts
rmi-pacta
pacta.loanbook:Easily Install and Load PACTA for Banks Packages
PACTA (Paris Agreement Capital Transition Assessment) for Banks is a tool that allows banks to calculate the climate alignment of their corporate lending portfolios. This package is designed to make it easy to install and load multiple PACTA for Banks packages in a single step. It also provides thorough documentation - the PACTA for Banks cookbook at <https://rmi-pacta.github.io/pacta.loanbook/articles/cookbook_overview.html> - on how to run a PACTA for Banks analysis. This covers prerequisites for the analysis, the separate steps of running the analysis, the interpretation of PACTA for Banks results, and advanced use cases.
Maintained by Jacob Kastl. Last updated 1 days ago.
1.7 match 1 stars 5.73 score 12 scripts
anthonypileggi
worrrd:Generate Wordsearch and Crossword Puzzles
Generate wordsearch and crossword puzzles using custom lists of words (and clues). Make them easy or hard, and print them to solve offline with paper and pencil!
Maintained by Anthony Pileggi. Last updated 2 years ago.
2.0 match 7 stars 4.66 score 13 scriptsbioc
PWMEnrich:PWM enrichment analysis
A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.
Maintained by Diego Diez. Last updated 5 months ago.
motifannotationsequencematchingsoftware
1.8 match 5.08 score 60 scripts
alexym1
fusionchartsR:Embedding FusionCharts in R
FusionCharts provides awesome and minimalist functions to make beautiful interactive charts <https://www.fusioncharts.com/>.
Maintained by Alex Yahiaoui Martinez. Last updated 3 months ago.
2.0 match 6 stars 4.40 score 42 scripts
jiaxiangbu
add2ggplot:Add to 'ggplot2'
Create 'ggplot2' themes and color palettes.
Maintained by Jiaxiang Li. Last updated 5 years ago.
2.0 match 4 stars 4.30 score 8 scriptsbioc
SPLINTER:Splice Interpreter of Transcripts
Provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.
Maintained by Diana Low. Last updated 5 months ago.
immunooncologygeneexpressionrnaseqvisualizationalternativesplicing
2.0 match 4.30 score 1 scripts
scholaempirica
reschola:The Schola Empirica Package
A collection of utilies, themes and templates for data analysis at Schola Empirica.
Maintained by Jan Netík. Last updated 5 months ago.
1.8 match 4 stars 4.83 score 14 scripts
iheid-library
iheiddown:For Writing Geneva Graduate Institute Documents
A set of tools for writing documents according to Geneva Graduate Institute conventions and regulations. The most common use is for writing and compiling theses or thesis chapters, as drafts or for examination with correct preamble formatting. However, the package also offers users to create HTML presentation slides with 'xaringan', complete problem sets, format posters, and, for course instructors, prepare a syllabus. The package includes additional functions for institutional color palettes, an institutional 'ggplot' theme, a function for counting manuscript words, and a bibliographical analysis toolkit.
Maintained by James Hollway. Last updated 2 years ago.
1.3 match 11 stars 6.14 score 5 scripts
tesselle
nexus:Sourcing Archaeological Materials by Chemical Composition
Exploration and analysis of compositional data in the framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This package provides tools for chemical fingerprinting and source tracking of ancient materials.
Maintained by Nicolas Frerebeau. Last updated 15 days ago.
archaeologyarchaeological-sciencearchaeometrycompositional-dataprovenance-studies
1.5 match 5.21 score 26 scripts 1 dependentsbioc
GladiaTOX:R Package for Processing High Content Screening data
GladiaTOX R package is an open-source, flexible solution to high-content screening data processing and reporting in biomedical research. GladiaTOX takes advantage of the tcpl core functionalities and provides a number of extensions: it provides a web-service solution to fetch raw data; it computes severity scores and exports ToxPi formatted files; furthermore it contains a suite of functionalities to generate pdf reports for quality control and data processing.
Maintained by PMP S.A. R Support. Last updated 5 months ago.
softwareworkflowstepnormalizationpreprocessingqualitycontrol
2.0 match 4.00 score 2 scriptstesselle
tabula:Analysis and Visualization of Archaeological Count Data
An easy way to examine archaeological count data. This package provides several tests and measures of diversity: heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.), richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and similarity (Brainerd-Robinson, etc.). It allows to easily visualize count data and statistical thresholds: rank vs abundance plots, heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.
Maintained by Nicolas Frerebeau. Last updated 16 days ago.
data-visualizationarchaeologyarchaeological-science
1.5 match 5.10 score 38 scripts 1 dependents
schochastics
Rokemon:Pokemon Style Plotting And Data
This package implements several themes for ggplot to bring your data into the world of Pokemon.
Maintained by David Schoch. Last updated 3 years ago.
1.9 match 94 stars 3.90 score 17 scripts
certe-medical-epidemiology
certestyle:A Certe R Package for Applying Certe Organisational Style
A Certe R Package for applying the organisational colours and style of Certe, plus some additional formatting functions. This package is part of the 'certedata' universe.
Maintained by Matthijs S. Berends. Last updated 9 months ago.
1.5 match 4.87 score 1 scripts 7 dependentstesselle
kairos:Analysis of Chronological Patterns from Archaeological Count Data
A toolkit for absolute and relative dating and analysis of chronological patterns. This package includes functions for chronological modeling and dating of archaeological assemblages from count data. It provides methods for matrix seriation. It also allows to compute time point estimates and density estimates of the occupation and duration of an archaeological site.
Maintained by Nicolas Frerebeau. Last updated 16 days ago.
chronologymatrix-seriationarchaeologyarchaeological-science
1.5 match 4.66 score 11 scripts 1 dependents
ashbaldry
video:'Shiny' Extension of 'video.js'
Video interactivity within 'shiny' applications using 'video.js'. Enables the status of the video to be sent from the UI to the server, and allows events such as playing and pausing the video to be triggered from the server.
Maintained by Ashley Baldry. Last updated 2 years ago.
1.0 match 6 stars 6.63 score 1.4k scripts
luizesser
chooseGCM:Selecting General Circulation Models for Species Distribution Modeling
Methods to help selecting General Circulation Models (GCMs) in the context of projecting models to future scenarios. It is provided clusterization algorithms, distance and correlation metrics, as well as a tailor-made algorithm to detect the optimum subset of GCMs that recreate the environment of all GCMs as proposed in Esser et al. (2025) <doi:10.1111/gcb.70008>.
Maintained by Luíz Esser. Last updated 22 days ago.
1.1 match 8 stars 6.23 score 5 scriptsrmi-pacta
pactaverse:Easily Install and Load the 'PACTA-verse'
The 'pactaverse' is a set of packages that work to help R users implement various functionality related to the PACTA open source project.
Maintained by Jackson Hoffart. Last updated 3 months ago.
1.8 match 6 stars 3.73 score 3 scripts
shixiangwang
CNVMotif:Explore, Analyze and Visualize Catalogs and Patterns of Copy Number Variation in Cancer Genomics
Provides functionality for exploring, analyzing and visualizing the copy number variation (CNV) motifs in cancer genomics.
Maintained by Shixiang Wang. Last updated 3 years ago.
3.7 match 1 stars 1.70 score 3 scriptsashbaldry
howler:'Shiny' Extension of 'howler.js'
Audio interactivity within 'shiny' applications using 'howler.js'. Enables the status of the audio player to be sent from the UI to the server, and events such as playing and pausing the audio can be triggered from the server.
Maintained by Ashley Baldry. Last updated 10 months ago.
1.0 match 16 stars 5.68 score 30 scripts
carlosyanez
customthemes:custom theming for ggplot, for personal use
Collection of (ggplot) theming options for personal use.
Maintained by Carlos Yanez Santibanez. Last updated 3 years ago.
3.4 match 1 stars 1.70 score 1 scripts
liuyu-star
ODRF:Oblique Decision Random Forest for Classification and Regression
The oblique decision tree (ODT) uses linear combinations of predictors as partitioning variables in a decision tree. Oblique Decision Random Forest (ODRF) is an ensemble of multiple ODTs generated by feature bagging. Oblique Decision Boosting Tree (ODBT) applies feature bagging during the training process of ODT-based boosting trees to ensemble multiple boosting trees. All three methods can be used for classification and regression, and ODT and ODRF serve as supplements to the classical CART of Breiman (1984) <DOI:10.1201/9781315139470> and Random Forest of Breiman (2001) <DOI:10.1023/A:1010933404324> respectively.
Maintained by Yu Liu. Last updated 5 months ago.
1.1 match 7 stars 5.10 score 18 scripts
cct-datascience
datadrivencv:Templates and helper functions for building a CV with spreadsheets
Separates the CV format from the content using spreadsheets, RMarkdown, and Pagedown. Built to allow easy out-of-the-box behavior, but also to allow you to go beyond the defaults with customization and lack of lock-in to a given format.
Maintained by Nick Strayer. Last updated 1 years ago.
1.9 match 2.59 score 39 scriptsbioc
ggmsa:Plot Multiple Sequence Alignment using 'ggplot2'
A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using 'ggplot2'. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as phylogenetic tree Visualized by 'ggtree', boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.
Maintained by Guangchuang Yu. Last updated 3 months ago.
softwarevisualizationalignmentannotationmultiplesequencealignment
0.5 match 209 stars 9.34 score 196 scripts 2 dependentstesselle
folio:Datasets for Teaching Archaeology and Paleontology
Datasets for teaching quantitative approaches and modeling in archaeology and paleontology. This package provides several types of data related to broad topics (cultural evolution, radiocarbon dating, paleoenvironments, etc.), which can be used to illustrate statistical methods in the classroom (multivariate data analysis, compositional data analysis, diversity measurement, etc.).
Maintained by Nicolas Frerebeau. Last updated 1 months ago.
archaeologyarchaeological-sciencepaleontologydatasets
1.5 match 3.02 score 2 scripts 1 dependents
grafxzahl
genBaRcode:Analysis and Visualization Tools for Genetic Barcode Data
Provides the necessary functions to identify and extract a selection of already available barcode constructs (Cornils, K. et al. (2014) <doi:10.1093/nar/gku081>) and freely choosable barcode designs from next generation sequence (NGS) data. Furthermore, it offers the possibility to account for sequence errors, the calculation of barcode similarities and provides a variety of visualisation tools (Thielecke, L. et al. (2017) <doi:10.1038/srep43249>).
Maintained by Lars Thielecke. Last updated 9 days ago.
2.0 match 2.30 score 6 scripts
cran
FourScores:A Game for Human vs. Human or Human vs. AI
A game for two players: Who gets first four in a row (horizontal, vertical or diagonal) wins. As board game published by Milton Bradley, designed by Howard Wexler and Ned Strongin.
Maintained by Matthias Speidel. Last updated 6 years ago.
4.5 match 1.00 score
nik01010
dashboardthemes:Customise the Appearance of 'shinydashboard' Applications using Themes
Allows manual creation of themes and logos to be used in applications created using the 'shinydashboard' package. Removes the need to change the underlying css code by wrapping it into a set of convenient R functions.
Maintained by Nik Lilovski. Last updated 3 years ago.
0.5 match 314 stars 8.60 score 424 scripts 2 dependents
rdinnager
rbff:R Interface to Boundary First Flattening Software (BFF)
Flatten 3D meshes into arbitrary 2D shapes using boundary first flattening (<https://github.com/GeometryCollective/boundary-first-flattening>).
Maintained by Russell Dinnage. Last updated 3 years ago.
1.8 match 5 stars 2.40 score 6 scripts
gabriel-assuncao
SIPDIBGE:Collection of Household Survey Packages Conducted by IBGE
Provides access to packages developed for downloading, reading and analyzing microdata from household surveys in Integrated System of Household Surveys - SIPD conducted by Brazilian Institute of Geography and Statistics - IBGE. More information can be obtained from the official website <https://www.ibge.gov.br/>.
Maintained by Gabriel Assuncao. Last updated 1 years ago.
1.8 match 2 stars 2.30 score
ashipunov
shipunov:Miscellaneous Functions from Alexey Shipunov
A collection of functions for data manipulation, plotting and statistical computing, to use separately or with the book "Visual Statistics. Use R!": Shipunov (2020) <http://ashipunov.info/shipunov/software/r/r-en.htm>. Dr Alexey Shipunov died in December 2022. Most useful functions: Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering; Recode() which does multiple recoding in a fast, simple and flexible way; Misclass() which outputs confusion matrix even if classes are not concerted; Overlap() which measures group separation on any projection; Biarrows() which converts any scatterplot into biplot; and Pleiad() which is fast and flexible correlogram.
Maintained by ORPHANED. Last updated 2 years ago.
4.1 match 1.00 score 9 scriptstesselle
tesselle:Easily Install and Load 'tesselle' Packages
Easy install and load key packages from the 'tesselle' suite in a single step. The 'tesselle' suite is a collection of packages for research and teaching in archaeology. These packages focus on quantitative analysis methods developed for archaeology. The 'tesselle' packages are designed to work seamlessly together and to complement general-purpose and other specialized statistical packages. These packages can be used to explore and analyze common data types in archaeology: count data, compositional data and chronological data. Learn more about 'tesselle' at <https://www.tesselle.org>.
Maintained by Nicolas Frerebeau. Last updated 16 days ago.
archaeological-sciencearchaeologystatistics
1.5 match 2.60 score 3 scripts
cynkra
indiedown:Individual R Markdown Templates
Simplifies the generation of customized R Markdown PDF templates. A template may include an individual logo, typography, geometry or color scheme. The package provides a skeleton with detailed instructions for customizations. The skeleton can be modified by changing defaults in the 'YAML' header, by adding additional 'LaTeX' commands or by applying dynamic adjustments in R. Individual corporate design elements, such as a title page, can be added as R functions that produce 'LaTeX' code.
Maintained by Christoph Sax. Last updated 3 months ago.
0.5 match 32 stars 7.84 score 3 scripts
gagolews
TurtleGraphics:Turtle Graphics
An implementation of turtle graphics <http://en.wikipedia.org/wiki/Turtle_graphics>. Turtle graphics comes from Papert's language Logo and has been used to teach concepts of computer programming.
Maintained by Marek Gagolewski. Last updated 3 years ago.
0.5 match 23 stars 7.21 score 117 scripts 2 dependents
txwri
twriTemplates:Templates for TWRI reports
Provides word and pdf Rmarkdown templates that meet TWRI branding guidance.
Maintained by Michael Schramm. Last updated 1 years ago.
2.0 match 1.78 score 12 scripts
hebrewseniorlife
memor:A 'rmarkdown' Template that Can be Highly Customized
A 'rmarkdown' template that supports company logo, contact info, watermarks and more. Currently restricted to 'Latex'/'Markdown'; a similar 'HTML' theme will be added in the future.
Maintained by Hao Zhu. Last updated 9 months ago.
0.5 match 90 stars 6.24 score 13 scripts
cedricbriandgithub
stacomiR:Fish Migration Monitoring
Graphical outputs and treatment for a database of fish pass monitoring. It is a part of the 'STACOMI' open source project developed in France by the French Office for Biodiversity institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See <http://stacomir.r-forge.r-project.org/> for more information on 'STACOMI'.
Maintained by Cedric Briand. Last updated 1 years ago.
1.1 match 1 stars 2.43 score 27 scripts
jameel-institute
jameelinst.rpkg.theme:A 'pkgdown' Template for Jameel Institute Packages
Package website colours and logos taken from the Imperial College London and Jameel Institute brand guidelines.
Maintained by Pratik Gupte. Last updated 5 months ago.
0.5 match 2.00 score
r3pos
ShinyWizard:An Interactive Wizard to Design, Build, and Deploy R Packages Demo Presentation
Design, build, and deploy R packages demo presentations by an interactive wizard. Set up unique title, logo and themes. Add personalized tabs exposing applicability. And deploy as a part of a package or an independent app.
Maintained by Rafal Urniaz. Last updated 5 months ago.
0.5 match 1.00 score