Showing 103 of total 103 results (show query)
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 4 days ago.
choropleth-mapsmapsspatialthematic-mapsvisualisation
879 stars 16.25 score 13k scripts 24 dependents
insightsengineering
teal:Exploratory Web Apps for Analyzing Clinical Trials Data
A 'shiny' based interactive exploration framework for analyzing clinical trials data. 'teal' currently provides a dynamic filtering facility and different data viewers. 'teal' 'shiny' applications are built using standard 'shiny' modules.
Maintained by Dawid Kaledkowski. Last updated 1 months ago.
clinical-trialsnestshinywebapp
206 stars 12.65 score 176 scripts 5 dependentsinsightsengineering
teal.modules.clinical:'teal' Modules for Standard Clinical Outputs
Provides user-friendly tools for creating and customizing clinical trial reports. By leveraging the 'teal' framework, this package provides 'teal' modules to easily create an interactive panel that allows for seamless adjustments to data presentation, thereby streamlining the creation of detailed and accurate reports.
Maintained by Dawid Kaledkowski. Last updated 1 months ago.
clinical-trialsmodulesnestoutputsshiny
35 stars 10.21 score 149 scripts
appsilon
shiny.react:Tools for Using React in Shiny
A toolbox for defining React component wrappers which can be used seamlessly in Shiny apps.
Maintained by Jakub Sobolewski. Last updated 11 months ago.
97 stars 10.20 score 83 scripts 4 dependentsappsilon
shiny.fluent:Microsoft Fluent UI for Shiny Apps
A rich set of UI components for building Shiny applications, including inputs, containers, overlays, menus, and various utilities. All components from Fluent UI (the underlying JavaScript library) are available and have usage examples in R.
Maintained by Jakub Sobolewski. Last updated 10 months ago.
microsoft-fluent-uireactrhinoverseshiny
281 stars 9.92 score 656 scripts
bioc
OmnipathR:OmniPath web service client and more
A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).
Maintained by Denes Turei. Last updated 1 months ago.
graphandnetworknetworkpathwayssoftwarethirdpartyclientdataimportdatarepresentationgenesignalinggeneregulationsystemsbiologytranscriptomicssinglecellannotationkeggcomplexesenzyme-ptmnetworksnetworks-biologyomnipathproteinsquarto
130 stars 9.90 score 226 scripts 2 dependents
cols4all
cols4all:Colors for all
Color palettes for all people, including those with color vision deficiency. Popular color palette series have been organized by type and have been scored on several properties such as color-blind-friendliness and fairness (i.e. do colors stand out equally?). Own palettes can also be loaded and analysed. Besides the common palette types (categorical, sequential, and diverging) it also includes cyclic and bivariate color palettes. Furthermore, a color for missing values is assigned to each palette.
Maintained by Martijn Tennekes. Last updated 2 months ago.
346 stars 9.87 score 26 dependentsinsightsengineering
teal.modules.general:General Modules for 'teal' Applications
Prebuilt 'shiny' modules containing tools for viewing data, visualizing data, understanding missing and outlier values within your data and performing simple data analysis. This extends 'teal' framework that supports reproducible research and analysis.
Maintained by Dawid Kaledkowski. Last updated 1 months ago.
general-purposemodulesnestshiny
13 stars 9.74 score 71 scriptsappsilon
shiny.telemetry:'Shiny' App Usage Telemetry
Enables instrumentation of 'Shiny' apps for tracking user session events such as input changes, browser type, and session duration. These events can be sent to any of the available storage backends and analyzed using the included 'Shiny' app to gain insights about app usage and adoption.
Maintained by André Veríssimo. Last updated 4 months ago.
67 stars 9.69 score 29 scripts
datawookie
emayili:Send Email Messages
A light, simple tool for sending emails with minimal dependencies.
Maintained by Andrew B. Collier. Last updated 2 months ago.
180 stars 9.59 score 95 scripts 3 dependents
e-sensing
sits:Satellite Image Time Series Analysis for Earth Observation Data Cubes
An end-to-end toolkit for land use and land cover classification using big Earth observation data, based on machine learning methods applied to satellite image data cubes, as described in Simoes et al (2021) <doi:10.3390/rs13132428>. Builds regular data cubes from collections in AWS, Microsoft Planetary Computer, Brazil Data Cube, Copernicus Data Space Environment (CDSE), Digital Earth Africa, Digital Earth Australia, NASA HLS using the Spatio-temporal Asset Catalog (STAC) protocol (<https://stacspec.org/>) and the 'gdalcubes' R package developed by Appel and Pebesma (2019) <doi:10.3390/data4030092>. Supports visualization methods for images and time series and smoothing filters for dealing with noisy time series. Includes functions for quality assessment of training samples using self-organized maps as presented by Santos et al (2021) <doi:10.1016/j.isprsjprs.2021.04.014>. Includes methods to reduce training samples imbalance proposed by Chawla et al (2002) <doi:10.1613/jair.953>. Provides machine learning methods including support vector machines, random forests, extreme gradient boosting, multi-layer perceptrons, temporal convolutional neural networks proposed by Pelletier et al (2019) <doi:10.3390/rs11050523>, and temporal attention encoders by Garnot and Landrieu (2020) <doi:10.48550/arXiv.2007.00586>. Supports GPU processing of deep learning models using torch <https://torch.mlverse.org/>. Performs efficient classification of big Earth observation data cubes and includes functions for post-classification smoothing based on Bayesian inference as described by Camara et al (2024) <doi:10.3390/rs16234572>, and methods for active learning and uncertainty assessment. Supports region-based time series analysis using package supercells <https://jakubnowosad.com/supercells/>. Enables best practices for estimating area and assessing accuracy of land change as recommended by Olofsson et al (2014) <doi:10.1016/j.rse.2014.02.015>. Minimum recommended requirements: 16 GB RAM and 4 CPU dual-core.
Maintained by Gilberto Camara. Last updated 2 months ago.
big-earth-datacbersearth-observationeo-datacubesgeospatialimage-time-seriesland-cover-classificationlandsatplanetary-computerr-spatialremote-sensingrspatialsatellite-image-time-seriessatellite-imagerysentinel-2stac-apistac-catalogcpp
494 stars 9.50 score 384 scriptsinsightsengineering
teal.slice:Filter Module for 'teal' Applications
Data filtering module for 'teal' applications. Allows for interactive filtering of data stored in 'data.frame' and 'MultiAssayExperiment' objects. Also displays filtered and unfiltered observation counts.
Maintained by Dawid Kaledkowski. Last updated 2 months ago.
11 stars 9.27 score 3 scripts 6 dependents
whipson
maestro:Orchestration of Data Pipelines
Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Maintained by Will Hipson. Last updated 9 hours ago.
120 stars 9.22 score 150 scriptsappsilon
rhino:A Framework for Enterprise Shiny Applications
A framework that supports creating and extending enterprise Shiny applications using best practices.
Maintained by Kamil Żyła. Last updated 10 hours ago.
306 stars 9.10 score 145 scriptsinsightsengineering
teal.transform:Functions for Extracting and Merging Data in the 'teal' Framework
A standardized user interface for column selection, that facilitates dataset merging in 'teal' framework.
Maintained by Dawid Kaledkowski. Last updated 2 months ago.
3 stars 8.39 score 9 scripts 4 dependentsinsightsengineering
teal.logger:Logging Setup for the 'teal' Family of Packages
Utilizing the 'logger' framework to record events within a package, specific to 'teal' family of packages. Supports logging namespaces, hierarchical logging, various log destinations, vectorization, and more.
Maintained by Dawid Kaledkowski. Last updated 2 months ago.
5 stars 8.24 score 3 scripts 8 dependents
nsaph-software
CausalGPS:Matching on Generalized Propensity Scores with Continuous Exposures
Provides a framework for estimating causal effects of a continuous exposure using observational data, and implementing matching and weighting on the generalized propensity score. Wu, X., Mealli, F., Kioumourtzoglou, M.A., Dominici, F. and Braun, D., 2022. Matching on generalized propensity scores with continuous exposures. Journal of the American Statistical Association, pp.1-29.
Maintained by Naeem Khoshnevis. Last updated 10 months ago.
24 stars 7.67 score 39 scripts
mdneuzerling
lambdr:Create a Runtime for Serving Containerised R Functions on 'AWS Lambda'
Runtime for serving containers that can execute R code on the 'AWS Lambda' serverless compute service <https://aws.amazon.com/lambda/>. Provides the necessary functionality for handling the various endpoints required for accepting new input and sending responses.
Maintained by David Neuzerling. Last updated 2 months ago.
138 stars 7.52 score 6 scripts
kharchenkolab
numbat:Haplotype-Aware CNV Analysis from scRNA-Seq
A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.
Maintained by Teng Gao. Last updated 13 days ago.
cancer-genomicscnv-detectionlineage-tracingphylogenysingle-cellsingle-cell-analysissingle-cell-rna-seqspatial-transcriptomicscpp
180 stars 7.48 score 120 scripts
ropensci
rsat:Dealing with Multiplatform Satellite Images
Downloading, customizing, and processing time series of satellite images for a region of interest. 'rsat' functions allow a unified access to multispectral images from Landsat, MODIS and Sentinel repositories. 'rsat' also offers capabilities for customizing satellite images, such as tile mosaicking, image cropping and new variables computation. Finally, 'rsat' covers the processing, including cloud masking, compositing and gap-filling/smoothing time series of images (Militino et al., 2018 <doi:10.3390/rs10030398> and Militino et al., 2019 <doi:10.1109/TGRS.2019.2904193>).
Maintained by Unai Pérez - Goya. Last updated 12 months ago.
54 stars 7.45 score 52 scripts
glenndavis52
spacesXYZ:CIE XYZ and some of Its Derived Color Spaces
Functions for converting among CIE XYZ, xyY, Lab, and Luv. Calculate Correlated Color Temperature (CCT) and the Planckian and daylight loci. The XYZs of some standard illuminants and some standard linear chromatic adaptation transforms (CATs) are included. Three standard color difference metrics are included, plus the forward direction of the 'CIECAM02' color appearance model.
Maintained by Glenn Davis. Last updated 2 months ago.
7.03 score 21 scripts 32 dependents
cldossantos
pacu:Precision Agriculture Computational Utilities
Support for a variety of commonly used precision agriculture operations. Includes functions to download and process raw satellite images from Sentinel-2 <https://documentation.dataspace.copernicus.eu/APIs/OData.html>. Includes functions that download vegetation index statistics for a given period of time, without the need to download the raw images <https://documentation.dataspace.copernicus.eu/APIs/SentinelHub/Statistical.html>. There are also functions to download and visualize weather data in a historical context. Lastly, the package also contains functions to process yield monitor data. These functions can build polygons around recorded data points, evaluate the overlap between polygons, clean yield data, and smooth yield maps.
Maintained by dos Santos Caio. Last updated 8 days ago.
13 stars 6.83 score 9 scripts
daroczig
botor:'AWS Python SDK' ('boto3') for R
Fork-safe, raw access to the 'Amazon Web Services' ('AWS') 'SDK' via the 'boto3' 'Python' module, and convenient helper functions to query the 'Simple Storage Service' ('S3') and 'Key Management Service' ('KMS'), partial support for 'IAM', the 'Systems Manager Parameter Store' and 'Secrets Manager'.
Maintained by Gergely Daróczi. Last updated 2 months ago.
amazon-web-servicesawsboto3python
30 stars 6.60 score 32 scripts
junjunlab
GseaVis:Implement for 'GSEA' Enrichment Visualization
Mark your interesting genes on plot and support more parameters to handle your own gene set enrichment analysis plot.
Maintained by Jun Zhang. Last updated 3 months ago.
146 stars 6.60 score 54 scripts
miracum
DQAstats:Core Functions for Data Quality Assessment
Perform data quality assessment ('DQA') of electronic health records ('EHR'). Publication: Kapsner et al. (2021) <doi:10.1055/s-0041-1733847>.
Maintained by Lorenz A. Kapsner. Last updated 14 hours ago.
9 stars 6.58 score 4 scripts 1 dependentsinsightsengineering
teal.goshawk:Longitudinal Visualization `teal` Modules
Modules that produce web interfaces through which longitudinal visualizations can be dynamically modified and displayed. These included box plot, correlation plot, density distribution plot, line plot, scatter plot and spaghetti plot with accompanying summary. Data are expected in ADaM structure. Requires analysis subject level (ADSL) and analysis laboratory (ADLB) data sets. Beyond core variables, Limit of Quantification flag variable (LOQFL) is expected with levels 'Y', 'N' or NA.
Maintained by Nick Paszty. Last updated 1 months ago.
3 stars 6.56 score 2 scripts
taxonomicallyinformedannotation
tima:Taxonomically Informed Metabolite Annotation
This package provides the infrastructure to perform Taxonomically Informed Metabolite Annotation.
Maintained by Adriano Rutz. Last updated 2 hours ago.
metabolite annotationchemotaxonomyscoring systemnatural productscomputational metabolomicstaxonomic distancespecialized metabolome
9 stars 6.55 score 32 scripts 2 dependentsnsaph-software
CRE:Interpretable Discovery and Inference of Heterogeneous Treatment Effects
Provides a new method for interpretable heterogeneous treatment effects characterization in terms of decision rules via an extensive exploration of heterogeneity patterns by an ensemble-of-trees approach, enforcing high stability in the discovery. It relies on a two-stage pseudo-outcome regression, and it is supported by theoretical convergence guarantees. Bargagli-Stoffi, F. J., Cadei, R., Lee, K., & Dominici, F. (2023) Causal rule ensemble: Interpretable Discovery and Inference of Heterogeneous Treatment Effects. arXiv preprint <doi:10.48550/arXiv.2009.09036>.
Maintained by Falco Joannes Bargagli Stoffi. Last updated 5 months ago.
13 stars 6.41 score 11 scripts
abhi-1u
texor:Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'
Articles in the 'R Journal' were first authored in 'LaTeX', which performs admirably for 'PDF' files but is less than ideal for modern online interfaces. The 'texor' package does all the transitional chores and conversions necessary to move to the online versions.
Maintained by Abhishek Ulayil. Last updated 3 hours ago.
7 stars 6.36 score 8 scriptsglenndavis52
colorSpec:Color Calculations with Emphasis on Spectral Data
Calculate with spectral properties of light sources, materials, cameras, eyes, and scanners. Build complex systems from simpler parts using a spectral product algebra. For light sources, compute CCT, CRI, SSI, and IES TM-30 reports. For object colors, compute optimal colors and Logvinenko coordinates. Work with the standard CIE illuminants and color matching functions, and read spectra from text files, including CGATS files. Estimate a spectrum from its response. A user guide and 9 vignettes are included.
Maintained by Glenn Davis. Last updated 2 months ago.
2 stars 6.34 score 73 scripts 5 dependents
aphalo
photobiologyInOut:Read Spectral and Logged Data from Foreign Files
Functions for reading, and in some cases writing, foreign files containing spectral data from spectrometers and their associated software, output from daylight simulation models in common use, and some spectral data repositories. As well as functions for exchange of spectral data with other R packages. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Maintained by Pedro J. Aphalo. Last updated 2 days ago.
6.32 score 63 scripts 1 dependents
alan-turing-institute
eider:Declarative Feature Extraction from Tabular Data Records
Extract features from tabular data in a declarative fashion, with a focus on processing medical records. Features are specified as JSON and are independently processed before being joined. Input data can be provided as CSV files or as data frames. This setup ensures that data is transformed in a modular and reproducible manner, and allows the same pipeline to be easily applied to new data.
Maintained by Camila Rangel Smith. Last updated 11 months ago.
3 stars 6.26 score 10 scripts
jbryer
login:'shiny' Login Module
Framework for adding authentication to 'shiny' applications. Provides flexibility as compared to other options for where user credentials are saved, allows users to create their own accounts, and password reset functionality. Bryer (2024) <doi:10.5281/zenodo.10987876>.
Maintained by Jason Bryer. Last updated 12 months ago.
21 stars 6.15 score 45 scripts
jeremygelb
geocmeans:Implementing Methods for Spatial Fuzzy Unsupervised Classification
Provides functions to apply spatial fuzzy unsupervised classification, visualize and interpret results. This method is well suited when the user wants to analyze data with a fuzzy clustering algorithm and to account for the spatial dimension of the dataset. In addition, indexes for estimating the spatial consistency and classification quality are proposed. The methods were originally proposed in the field of brain imagery (seed Cai and al. 2007 <doi:10.1016/j.patcog.2006.07.011> and Zaho and al. 2013 <doi:10.1016/j.dsp.2012.09.016>) and recently applied in geography (see Gelb and Apparicio <doi:10.4000/cybergeo.36414>).
Maintained by Jeremy Gelb. Last updated 5 months ago.
clusteringcmeansfuzzy-classification-algorithmsspatial-analysisspatial-fuzzy-cmeansunsupervised-learningcppopenmp
28 stars 6.10 score 90 scriptsbioc
shiny.gosling:A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization for R and Shiny
A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. http://gosling-lang.org/. This R package is based on gosling.js. It uses R functions to create gosling plots that could be embedded onto R Shiny apps.
Maintained by Appsilon. Last updated 5 months ago.
shinyappsgeneticsvisualization
6.08 score 53 scripts 1 dependentsbioc
RMassBank:Workflow to process tandem MS files and build MassBank records
Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.
Maintained by RMassBank at Eawag. Last updated 5 months ago.
immunooncologybioinformaticsmassspectrometrymetabolomicssoftwareopenjdk
6.02 score 26 scripts
eu-ecdc
epitweetr:Early Detection of Public Health Threats from 'Twitter' Data
It allows you to automatically monitor trends of tweets by time, place and topic aiming at detecting public health threats early through the detection of signals (e.g. an unusual increase in the number of tweets). It was designed to focus on infectious diseases, and it can be extended to all hazards or other fields of study by modifying the topics and keywords. More information is available in the 'epitweetr' peer-review publication (doi:10.2807/1560-7917.ES.2022.27.39.2200177).
Maintained by Laura Espinosa. Last updated 1 years ago.
early-warning-systemsepidemic-surveillancelucenemachine-learningsignal-detectionsparktwitter
56 stars 5.98 score 86 scriptsnsaph-software
GPCERF:Gaussian Processes for Estimating Causal Exposure Response Curves
Provides a non-parametric Bayesian framework based on Gaussian process priors for estimating causal effects of a continuous exposure and detecting change points in the causal exposure response curves using observational data. Ren, B., Wu, X., Braun, D., Pillai, N., & Dominici, F.(2021). "Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes." arXiv preprint <doi:10.48550/arXiv.2105.03454>.
Maintained by Boyu Ren. Last updated 11 months ago.
9 stars 5.86 score 16 scriptsbioc
sangeranalyseR:sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.
Maintained by Kuan-Hao Chao. Last updated 30 days ago.
geneticsalignmentsequencingsangerseqpreprocessingqualitycontrolvisualizationgui
5.76 score 46 scripts
statisticspoland
bdl:Interface and Tools for 'BDL' API
Interface to Local Data Bank ('Bank Danych Lokalnych' - 'bdl') API <https://api.stat.gov.pl/Home/BdlApi?lang=en> with set of useful tools like quick plotting and map generating using data from bank.
Maintained by Krzysztof Kania. Last updated 2 years ago.
20 stars 5.74 score 11 scriptsdaroczig
fbRads:Analyzing and Managing Facebook Ads from R
Wrapper functions around the Facebook Marketing 'API' to create, read, update and delete custom audiences, images, campaigns, ad sets, ads and related content.
Maintained by Gergely Daroczi. Last updated 1 years ago.
adtechfacebookfacebook-adsfacebook-apifacebook-marketing-apimarketing
153 stars 5.72 score 17 scriptsabhi-1u
rebib:Convert and Aggregate Bibliographies
Authors working with 'LaTeX' articles use the built-in bibliography options and 'BibTeX' files. While this might work with 'LaTeX', it does not function well with Web articles. As a way out, 'rebib' offers tools to convert and combine bibliographies from both sources.
Maintained by Abhishek Ulayil. Last updated 6 months ago.
1 stars 5.68 score 9 scripts 1 dependents
michaelgruenstaeudl
PACVr:Plastome Assembly Coverage Visualization
Visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes. For more information, please see Gruenstaeudl and Jenke (2020) <doi:10.1186/s12859-020-3475-0>.
Maintained by Michael Gruenstaeudl. Last updated 4 months ago.
3 stars 5.61 score 5 scriptsinsightsengineering
teal.modules.hermes:RNA-Seq Analysis Modules to Add to a Teal Application
RNA-seq analysis teal modules based on the `hermes` package.
Maintained by Daniel Sabanés Bové. Last updated 1 years ago.
7 stars 5.54 score 32 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.
23 stars 5.54 score 6 scripts
difm-brain
ofpetrial:Design on-Farm Precision Field Agronomic Trials
A comprehensive system for designing and implementing on-farm precision field agronomic trials. You provide field data, tell 'ofpetrial' how to design a trial, and get readily-usable trial design files and a report checks the validity and reliability of the trial design.
Maintained by Taro Mieno. Last updated 4 months ago.
3 stars 5.49 score 23 scripts
md-anderson-bioinformatics
NGCHM:Next Generation Clustered Heat Maps
Next-Generation Clustered Heat Maps (NG-CHMs) allow for dynamic exploration of heat map data in a web browser. 'NGCHM' allows users to create both stand-alone HTML files containing a Next-Generation Clustered Heat Map, and .ngchm files to view in the NG-CHM viewer. See Ryan MC, Stucky M, et al (2020) <doi:10.12688/f1000research.20590.2> for more details.
Maintained by Mary A Rohrdanz. Last updated 25 days ago.
9 stars 5.48 score 28 scripts
cadam00
priorCON:Graph Community Detection Methods into Systematic Conservation Planning
An innovative tool-set that incorporates graph community detection methods into systematic conservation planning. It is designed to enhance spatial prioritization by focusing on the protection of areas with high ecological connectivity. Unlike traditional approaches that prioritize individual planning units, 'priorCON' focuses on clusters of features that exhibit strong ecological linkages. The 'priorCON' package is built upon the 'prioritizr' package <doi:10.32614/CRAN.package.prioritizr>, using commercial and open-source exact algorithm solvers that ensure optimal solutions to prioritization problems.
Maintained by Christos Adam. Last updated 2 months ago.
biodiversitycommunity-detectionconservationconservation-planninggraph-theoryprioritization
3 stars 5.37 score 13 scripts
krzjoa
path.chain:Concise Structure for Chainable Paths
Provides path_chain class and functions, which facilitates loading and saving directory structure in YAML configuration files via 'config' package. The file structure you created during exploration can be transformed into legible section in the config file, and then easily loaded for further usage.
Maintained by Krzysztof Joachimiak. Last updated 6 months ago.
10 stars 5.34 score 11 scriptsropensci
roreviewapi:Plumber API to report package structure and function
Plumber API to report package structure and function.
Maintained by Mark Padgham. Last updated 1 months ago.
4 stars 5.26 scoreaphalo
ooacquire:Acquire Data from OO Spectrometers
Functions to acquire data directly from Ocean Optics spectrometers, and functions to read similar data from files. Functions to convert raw-counts into counts-per-second and physical quantities. Data are saved in objects of classes defined in package 'photobiology'. The instrument settings, instrument description, date-time of acquisition and optionally goecode are stored as attributes.
Maintained by Pedro J. Aphalo. Last updated 2 days ago.
data-acquisitiondata-importr4photobiologyspectracpp
1 stars 5.11 score 93 scriptsdaroczig
binancer:API Client to 'Binance'
R client to the 'Binance' Public Rest API for data collection on cryptocurrencies, portfolio management and trading: <https://github.com/binance/binance-spot-api-docs/blob/master/rest-api.md>.
Maintained by Gergely Daróczi. Last updated 1 years ago.
apibinancebinance-apibitcoinblockchaincryptocurrency
53 stars 5.11 score 49 scriptsinsightsengineering
teal.osprey:'teal' Modules for TLG Functions in Osprey
Community efforts to collect 'teal' modules for TLGs defined in 'osprey' package. Enables 'teal' app developers to create 'shiny' applications with a use of 'osprey' analysis functions.
Maintained by Nina Qi. Last updated 1 months ago.
5 stars 5.05 score 1 scriptsmiracum
DIZutils:Utilities for 'DIZ' R Package Development
Utility functions used for the R package development infrastructure inside the data integration centers ('DIZ') to standardize and facilitate repetitive tasks such as setting up a database connection or issuing notification messages and to avoid redundancy.
Maintained by Jonathan M. Mang. Last updated 4 months ago.
3 stars 5.03 score 5 scripts 2 dependentsbioc
seahtrue:Seahtrue revives XF data for structured data analysis
Seahtrue organizes oxygen consumption and extracellular acidification analysis data from experiments performed on an XF analyzer into structured nested tibbles.This allows for detailed processing of raw data and advanced data visualization and statistics. Seahtrue introduces an open and reproducible way to analyze these XF experiments. It uses file paths to .xlsx files. These .xlsx files are supplied by the userand are generated by the user in the Wave software from Agilent from the assay result files (.asyr). The .xlsx file contains different sheets of important data for the experiment; 1. Assay Information - Details about how the experiment was set up. 2. Rate Data - Information about the OCR and ECAR rates. 3. Raw Data - The original raw data collected during the experiment. 4. Calibration Data - Data related to calibrating the instrument. Seahtrue focuses on getting the specific data needed for analysis. Once this data is extracted, it is prepared for calculations through preprocessing. To make sure everything is accurate, both the initial data and the preprocessed data go through thorough checks.
Maintained by Vincent de Boer. Last updated 5 months ago.
cellbasedassaysfunctionalpredictiondatarepresentationdataimportcellbiologycheminformaticsmetabolomicsmicrotitreplateassayvisualizationqualitycontrolbatcheffectexperimentaldesignpreprocessinggo
5.00 score 2 scripts
xtimbeau
sourcoise:Source a Script and Cache
Provides a function that behaves nearly as base::source() but implements a caching mechanism on disk, project based. It allows to quasi source() R scripts that gather data but can fail or consume to much time to respond even if nothing new is expected. It comes with tools to check and execute on demand or when cache is invalid the script.
Maintained by Xavier Timbeau. Last updated 2 days ago.
1 stars 4.88 score
mazamascience
MazamaSpatialPlots:Thematic Plots for Mazama Spatial Datasets
A suite of convenience functions for generating US state and county thematic maps using datasets from the MazamaSpatialUtils package.
Maintained by Jonathan Callahan. Last updated 2 months ago.
4.84 score 23 scripts
bioc
gINTomics:Multi-Omics data integration
gINTomics is an R package for Multi-Omics data integration and visualization. gINTomics is designed to detect the association between the expression of a target and of its regulators, taking into account also their genomics modifications such as Copy Number Variations (CNV) and methylation. What is more, gINTomics allows integration results visualization via a Shiny-based interactive app.
Maintained by Angelo Velle. Last updated 5 months ago.
geneexpressionrnaseqmicroarrayvisualizationcopynumbervariationgenetargetquarto
3 stars 4.78 score 3 scripts
mharinga
spatialrisk:Calculating Spatial Risk
Methods for spatial risk calculations. It offers an efficient approach to determine the sum of all observations within a circle of a certain radius. This might be beneficial for insurers who are required (by a recent European Commission regulation) to determine the maximum value of insured fire risk policies of all buildings that are partly or fully located within a circle of a radius of 200m. See Church (1974) <doi:10.1007/BF01942293> for a description of the problem.
Maintained by Martin Haringa. Last updated 7 months ago.
actuarial-scienceinsurancesolvency-iispatialcpp
19 stars 4.76 score 30 scriptsmiracum
DIZtools:Lightweight Utilities for 'DIZ' R Package Development
Lightweight utility functions used for the R package development infrastructure inside the data integration centers ('DIZ') to standardize and facilitate repetitive tasks such as setting up a database connection or issuing notification messages and to avoid redundancy.
Maintained by Jonathan M. Mang. Last updated 14 days ago.
3 stars 4.73 score 2 scripts 3 dependents
dfsp-spirit
wal:Read and Write 'wal' Bitmap Image Files and Other 'Quake' Assets
Read 'Quake' assets including bitmap images and textures in 'wal' file format. This package also provides support for extracting these assets from 'WAD' and 'PAK' file archives. It can also read models in 'MDL' and 'MD2' formats.
Maintained by Tim Schäfer. Last updated 1 years ago.
imagepakquakequake-enginequake2textureswadwal
10 stars 4.70 score 1 scripts
mrchypark
sendgridr:Mail Sender Using 'Sendgrid' Service
Send email using 'Sendgrid' <https://sendgrid.com/en-us> mail API(v3) <https://docs.sendgrid.com/api-reference/how-to-use-the-sendgrid-v3-api/authentication>.
Maintained by Chanyub Park. Last updated 1 years ago.
hacktoberfesthacktoberfest2021mailmailersendgrid
23 stars 4.66 score 10 scriptsbioc
dce:Pathway Enrichment Based on Differential Causal Effects
Compute differential causal effects (dce) on (biological) networks. Given observational samples from a control experiment and non-control (e.g., cancer) for two genes A and B, we can compute differential causal effects with a (generalized) linear regression. If the causal effect of gene A on gene B in the control samples is different from the causal effect in the non-control samples the dce will differ from zero. We regularize the dce computation by the inclusion of prior network information from pathway databases such as KEGG.
Maintained by Kim Philipp Jablonski. Last updated 4 months ago.
softwarestatisticalmethodgraphandnetworkregressiongeneexpressiondifferentialexpressionnetworkenrichmentnetworkkeggbioconductorcausality
13 stars 4.59 score 4 scripts
rinterface
shinyNextUI:'HeroUI' 'React' Template for 'shiny' Apps
A set of user interface components to create outstanding 'shiny' apps <https://shiny.posit.co/>, with the power of 'React' 'JavaScript' <https://react.dev/>. Seamlessly support dark and light themes, customize CSS with 'tailwind' <https://tailwindcss.com/>.
Maintained by David Granjon. Last updated 15 days ago.
26 stars 4.41 scorer-tmap
tmap.cartogram:Extension to 'tmap' for Creating Cartograms
Provides new layer functions to 'tmap' for creating various types of cartograms. A cartogram is a type of thematic map in which geographic areas are resized or distorted based on a quantitative variable, such as population. The goal is to make the area sizes proportional to the selected variable while preserving geographic positions as much as possible.
Maintained by Martijn Tennekes. Last updated 27 days ago.
1 stars 4.40 score 1 scripts
dipterix
ravedash:Dashboard System for Reproducible Visualization of 'iEEG'
Dashboard system to display the analysis results produced by 'RAVE' (Magnotti J.F., Wang Z., Beauchamp M.S. (2020), Reproducible analysis and visualizations of 'iEEG' <doi:10.1016/j.neuroimage.2020.117341>). Provides infrastructure to integrate customized analysis pipelines into dashboard modules, including file structures, front-end widgets, and event handlers.
Maintained by Zhengjia Wang. Last updated 5 months ago.
1 stars 4.35 score 45 scriptsglenndavis52
munsellinterpol:Interpolate Munsell Renotation Data from Hue Value/Chroma to CIE/RGB
Methods for interpolating data in the Munsell color system following the ASTM D-1535 standard. Hues and chromas with decimal values can be interpolated and converted to/from the Munsell color system and CIE xyY, CIE XYZ, CIE Lab, CIE Luv, or RGB. Includes ISCC-NBS color block lookup. Based on the work by Paul Centore, "The Munsell and Kubelka-Munk Toolbox".
Maintained by Glenn Davis. Last updated 2 months ago.
2 stars 4.31 score 43 scripts 2 dependentsbioc
wppi:Weighting protein-protein interactions
Protein-protein interaction data is essential for omics data analysis and modeling. Database knowledge is general, not specific for cell type, physiological condition or any other context determining which connections are functional and contribute to the signaling. Functional annotations such as Gene Ontology and Human Phenotype Ontology might help to evaluate the relevance of interactions. This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.
Maintained by Ana Galhoz. Last updated 5 months ago.
graphandnetworknetworkpathwayssoftwaregenesignalinggenetargetsystemsbiologytranscriptomicsannotationgene-ontologygene-prioritizationhuman-phenotype-ontologyomnipathppi-networksrandom-walk-with-restartquarto
1 stars 4.30 score 4 scripts
rohelab
fastadi:Self-Tuning Data Adaptive Matrix Imputation
Implements the AdaptiveImpute matrix completion algorithm of 'Intelligent Initialization and Adaptive Thresholding for Iterative Matrix Completion', <https://amstat.tandfonline.com/doi/abs/10.1080/10618600.2018.1518238>. AdaptiveImpute is useful for embedding sparsely observed matrices, often out performs competing matrix completion algorithms, and self-tunes its hyperparameter, making usage easy.
Maintained by Alex Hayes. Last updated 9 months ago.
9 stars 4.26 score 6 scriptsmiracum
DQAgui:Graphical User Interface for Data Quality Assessment
A graphical user interface (GUI) to the functions implemented in the R package 'DQAstats'. Publication: Mang et al. (2021) <doi:10.1186/s12911-022-01961-z>.
Maintained by Lorenz A. Kapsner. Last updated 2 months ago.
2 stars 4.15 score 10 scripts
calfarog
GREENeR:Geospatial Regression Equation for European Nutrient Losses (GREEN)
Tools and methods to apply the model Geospatial Regression Equation for European Nutrient losses (GREEN); Grizzetti et al. (2005) <doi:10.1016/j.jhydrol.2004.07.036>; Grizzetti et al. (2008); Grizzetti et al. (2012) <doi:10.1111/j.1365-2486.2011.02576.x>; Grizzetti et al. (2021) <doi:10.1016/j.gloenvcha.2021.102281>.
Maintained by C. Alfaro. Last updated 7 months ago.
calibrationgeospatialnutrientplots
1 stars 4.00 score 9 scripts
rmi-pacta
pacta.data.scraping:Scrapes data from various web sources needed for PACTA
This package provides tools to scrape data from various web sources needed for PACTA.
Maintained by CJ Yetman. Last updated 5 months ago.
climate-changepactapactaversesustainable-finance
2 stars 3.86 score 3 scripts 1 dependentsrmi-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 4 months ago.
6 stars 3.73 score 3 scripts
atalv
azlogr:Logging in 'R' and Post to 'Azure Log Analytics' Workspace
It extends the functionality of 'logger' package. Additional logging metadata can be configured to be collected. Logging messages are displayed on console and optionally they are sent to 'Azure Log Analytics' workspace in real-time.
Maintained by Vivek Atal. Last updated 1 years ago.
azureazure-log-analyticslogging
3.70 score 8 scripts
cran
shiny.blueprint:Palantir's 'Blueprint' for 'Shiny' Apps
Easily use 'Blueprint', the popular 'React' library from Palantir, in your 'Shiny' app. 'Blueprint' provides a rich set of UI components for creating visually appealing applications and is optimized for building complex, data-dense web interfaces. This package provides most components from the underlying library, as well as special wrappers for some components to make it easy to use them in 'R' without writing 'JavaScript' code.
Maintained by Jakub Sobolewski. Last updated 11 months ago.
3.70 scoredatawookie
clockify:A Wrapper for the 'Clockify' API
A wrapper for the Clockify API <https://docs.clockify.me/>, making it possible to query, insert and update time keeping data.
Maintained by Andrew B. Collier. Last updated 10 months ago.
1 stars 3.65 score 6 scripts
litgde
Spectran:Visual and Non-Visual Spectral Analysis of Light
Analyse light spectra for visual and non-visual (often called melanopic) needs, wrapped up in a Shiny App. 'Spectran' allows for the import of spectra in various CSV forms but also provides a wide range of example spectra and even the creation of own spectral power distributions. The goal of the app is to provide easy access and a visual overview of the spectral calculations underlying common parameters used in the field. It is thus ideal for educational purposes or the creation of presentation ready graphs in lighting research and application. 'Spectran' uses equations and action spectra described in CIE S026 (2018) <doi:10.25039/S026.2018>, DIN/TS 5031-100 (2021) <doi:10.31030/3287213>, and ISO/CIE 23539 (2023) <doi:10.25039/IS0.CIE.23539.2023>.
Maintained by Johannes Zauner. Last updated 6 months ago.
2 stars 3.60 score 3 scripts
fgu5tav0
OxSR:Soil Iron Oxides via Diffuse Reflectance
Calculate the ratio of iron oxides, hematite and goethite, in soil using the diffuse reflectance technique. The Kubelka-Munk theory, second derivative analysis, and spectral region amplitudes related to hematite and goethite content are used for quantification (Torrent, J., & Barron, V. (2008) <doi:10.2136/sssabookser5.5.c13>). Additionally, the package calculates soil color in the visible spectrum using Munsell and RGB color spaces, based on color theory (Viscarra et al. (2006) <doi:10.1016/j.geoderma.2005.07.017>).
Maintained by Gustavo Frosi. Last updated 15 days ago.
3.54 score
aymennasri
tndata:Fetch Datasets from the Official Tunisian Data Catalog
Simplifies access to Tunisian government open data from <https://data.gov.tn/fr/>. Queries datasets by theme, author, or keywords, retrieves metadata, and gets structured results ready for analysis; all through the official 'CKAN' API.
Maintained by Aymen Nasri. Last updated 9 days ago.
3.40 scoreropensci
ReLTER:An Interface for the eLTER Community
ReLTER provides access to DEIMS-SDR (https://deims.org/), and allows interaction with data and software implemented by eLTER Research Infrastructure (RI) thus improving data sharing among European LTER projects. ReLTER uses the R language to access and interact with the DEIMS-SDR archive of information shared by the Long Term Ecological Research (LTER) network. This package grew within eLTER H2020 as a major project that will help advance the development of European Long-Term Ecosystem Research Infrastructures (eLTER RI - https://elter-ri.eu). The ReLTER package functions in particular allow to: - retrieve the information about entities (e.g. sites, datasets, and activities) shared by DEIMS-SDR (see e.g. get_site_info function); - interact with the [ODSEurope](maps.opendatascience.eu) starting with the dataset shared by [DEIMS-SDR](https://deims.org/) (see e.g. [get_site_ODS](https://docs.ropensci.org/ReLTER/reference/get_site_ODS.html) function); - use the eLTER site informations to download and crop geospatial data from other platforms (see e.g. get_site_ODS function); - improve the quality of the dataset (see e.g. get_id_worms). Functions currently implemented are derived from discussions of the needs among the eLTER users community. The ReLTER package will continue to follow the progress of eLTER-RI and evolve, adding new tools and improvements as required.
Maintained by Alessandro Oggioni. Last updated 1 years ago.
biodiversity-informaticsdata-scienceecologyelterresearch-infrastructure
12 stars 3.38 score 4 scripts
e-sensing
bayesEO:Bayesian Smoothing of Remote Sensing Image Classification
A Bayesian smoothing method for post-processing of remote sensing image classification which refines the labelling in a classified image in order to enhance its classification accuracy. Combines pixel-based classification methods with a spatial post-processing method to remove outliers and misclassified pixels.
Maintained by Gilberto Camara. Last updated 10 months ago.
4 stars 3.30 score 6 scriptsglenndavis52
spacesRGB:Standard and User-Defined RGB Color Spaces, with Conversion Between RGB and CIE XYZ and Lab
Standard RGB spaces included are sRGB, 'Adobe' RGB, 'ProPhoto' RGB, BT.709, and others. User-defined RGB spaces are also possible. There is partial support for ACES Color workflows.
Maintained by Glenn Davis. Last updated 3 months ago.
3.30 score 11 scripts 3 dependents
ddorch
Rthingsboard:'ThingsBoard' API
The goal of 'Rthingsboard' is to provide interaction with the API of 'ThingsBoard' (<https://thingsboard.io/>), an open-source IoT platform for device management, data collection, processing and visualization.
Maintained by David Dorchies. Last updated 3 years ago.
3 stars 3.18 score 2 scripts
nenuial
geographer:Geography Vizualisations
Provides function and objects to establish vizualisations for my Geography lessons.
Maintained by Pascal Burkhard. Last updated 1 months ago.
2 stars 3.08 scoreglenndavis52
zonohedra:Compute and Plot Zonohedra from Vector Generators
Computes a zonohedron from real vector generators. The package also computes zonogons (2D zonotopes) and zonosegs (1D zonotopes). An elementary S3 class for matroids is included, which supports matroids with rank 3, 2, and 1. Optimization methods are taken from Heckbert (1985) <https://www.cs.cmu.edu/~ph/zono.ps.gz>.
Maintained by Glenn Davis. Last updated 2 months ago.
3.00 score 8 scripts
tombishop1
itraxR:Itrax Data Analysis Tools
Parse, trim, join, visualise and analyse data from Itrax sediment core multi-parameter scanners manufactured by Cox Analytical Systems, Sweden. Functions are provided for parsing XRF-peak area files, line-scan optical images, and radiographic images, alongside accompanying metadata. A variety of data wrangling tasks like trimming, joining and reducing XRF-peak area data are simplified. Multivariate methods are implemented with appropriate data transformation.
Maintained by Thomas Bishop. Last updated 10 months ago.
5 stars 3.00 score 1 scriptsdatawookie
filebin:Wrapper for the Filebin File Sharing API
A wrapper for the Filebin API. Filebin implements convenient file sharing on the web.
Maintained by Andrew B. Collier. Last updated 2 years ago.
2 stars 3.00 score 3 scripts
mikejohnson51
climateR.catalogs:
A collection of tools for maniputatling hydrologic and hydraulic networks
Maintained by Mike Johnson. Last updated 1 years ago.
16 stars 2.90 score 1 scripts
owp-spatial
reference.fabric:Hydrological Reference Fabric Tools
Development tools and `targets` pipeline for generating a national hydrological geospatial reference fabric.
Maintained by Justin Singh-Mohudpur. Last updated 2 months ago.
1 stars 2.90 score
nowosad
geostatbook:Geostatystyka w R
Materialy do skryptu Geostatystyka w R.
Maintained by Jakub Nowosad. Last updated 3 years ago.
6 stars 2.88 score 25 scripts
myaseen208
ppcSpatial:Spatial Analysis of Pakistan Population Census
Spatial Analysis for exploration of Pakistan Population Census 2017 (<http://www.pbscensus.gov.pk/>). It uses data from R package 'PakPC2017'.
Maintained by Muhammad Yaseen. Last updated 2 years ago.
2.70 score 3 scriptscran
bangladesh:Provides Ready to Use Shapefiles for Geographical Map of Bangladesh
Usually, it is difficult to plot choropleth maps for Bangladesh in 'R'. The 'bangladesh' package provides ready-to-use shapefiles for different administrative regions of Bangladesh (e.g., Division, District, Upazila, and Union). This package helps users to draw thematic maps of administrative regions of Bangladesh easily as it comes with the 'sf' objects for the boundaries. It also provides functions allowing users to efficiently get specific area maps and center coordinates for regions. Users can also search for a specific area and calculate the centroids of those areas.
Maintained by Musaddiqur Rahman Ovi. Last updated 2 years ago.
1 stars 2.70 score
ecamenen
MainExistingDatasets:Main Existing Human Datasets
Shiny for Open Science to visualize, share, and inventory the main existing human datasets for researchers.
Maintained by Etienne Camenen. Last updated 2 years ago.
biomedicalinformaticsdatarepresentationvisualization
2.70 score 1 scripts
marioangst
rayab:R package for AYAB compatible images
Functionality to create images suitable for two-color knitting via the AYAB (all yarns are beautiful) open source software/ hardware project from plots, text and images.
Maintained by Mario Angst. Last updated 4 months ago.
1 stars 2.70 score 5 scripts
adafede
CentroidR:CentroidR
CentroidR provides the infrastructure to centroid profile spectra.
Maintained by Adriano Rutz. Last updated 4 days ago.
2.60 scorecran
LabourMarketAreas:Identification, Tuning, Visualisation and Analysis of Labour Market Areas
Produces Labour Market Areas from commuting flows available at elementary territorial units. It provides tools for automatic tuning based on spatial contiguity. It also allows for statistical analyses and visualisation of the new functional geography.
Maintained by Luisa Franconi. Last updated 1 years ago.
2.00 score
fdzul
boldenr:boldenr: a package designed to generate of Dengue Bulletin of Veracruz state
This package contains functions designed specifically to generate graphs, tables, heatmap, maps and hotspots that allow designing the dengue bulletin of the state of Veracruz.
Maintained by The package maintainer. Last updated 12 months ago.
1 stars 1.81 score 13 scripts
workshop-brg
abmR:Agent-Based Models in R
Supplies tools for running agent-based models (ABM) in R, as discussed in Gochanour et al. (2022) <doi:10.1111/2041-210X.14014>. The package contains two movement functions, each of which is based on the Ornstein-Uhlenbeck (OU) model (Ornstein & Uhlenbeck, 1930) <doi:10.1103/PhysRev.36.823>. It also contains several visualization and data summarization functions to facilitate the presentation of simulation results.
Maintained by Benjamin Gochanour. Last updated 2 years ago.
1 stars 1.70 score
cran
interfr:Interference Color Charts for Polarized Light Microscopy
Computes interference color tables and plots customized Michel-Levy or Raith-Sorensen charts. Automatic interpretation of polarized-light microscopy images is still under development and will come soon.
Maintained by Olivier Eterradossi. Last updated 8 years ago.
1 stars 1.00 score