R-universe search: needs:V8

rstudio

gt:Easily Create Presentation-Ready Display Tables

Build display tables from tabular data with an easy-to-use set of functions. With its progressive approach, we can construct display tables with a cohesive set of table parts. Table values can be formatted using any of the included formatting functions. Footnotes and cell styles can be precisely added through a location targeting system. The way in which 'gt' handles things for you means that you don't often have to worry about the fine details.

Maintained by Richard Iannone. Last updated 24 days ago.

docx easy-to-use html latex rtf summary-tables

2.1k stars 18.36 score 20k scripts 112 dependents

ddsjoberg

gtsummary:Presentation-Ready Data Summary and Analytic Result Tables

Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers.

Maintained by Daniel D. Sjoberg. Last updated 4 days ago.

easy-to-use gt html5 regression-models reproducibility reproducible-research statistics summary-statistics summary-tables table1 tableone

1.1k stars 17.02 score 8.2k scripts 15 dependents

keaven

gsDesign:Group Sequential Design

Derives group sequential clinical trial designs and describes their properties. Particular focus on time-to-event, binary, and continuous outcomes. Largely based on methods described in Jennison, Christopher and Turnbull, Bruce W., 2000, "Group Sequential Methods with Applications to Clinical Trials" ISBN: 0-8493-0316-8.

Maintained by Keaven Anderson. Last updated 25 days ago.

biostatistics boundaries clinical-trials design spending-functions

51 stars 13.05 score 338 scripts 5 dependents

jtextor

dagitty:Graphical Analysis of Structural Causal Models

A port of the web-based software 'DAGitty', available at <https://dagitty.net>, for analyzing structural causal models (also known as directed acyclic graphs or DAGs). This package computes covariate adjustment sets for estimating causal effects, enumerates instrumental variables, derives testable implications (d-separation and vanishing tetrads), generates equivalent models, and includes a simple facility for data simulation.

Maintained by Johannes Textor. Last updated 4 months ago.

302 stars 12.83 score 1.7k scripts 11 dependents

r-causal

ggdag:Analyze and Create Elegant Directed Acyclic Graphs

Tidy, analyze, and plot directed acyclic graphs (DAGs). 'ggdag' is built on top of 'dagitty', an R package that uses the 'DAGitty' web tool (<https://dagitty.net/>) for creating and analyzing DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty' objects using 'ggplot2' and 'ggraph', as well as common analytic and graphical functions, such as determining adjustment sets and node relationships.

Maintained by Malcolm Barrett. Last updated 8 months ago.

causal-inference dag ggplot-extension

443 stars 11.78 score 1.8k scripts 5 dependents

ateucher

rmapshaper:Client for 'mapshaper' for 'Geospatial' Operations

Edit and simplify 'geojson', 'Spatial', and 'sf' objects. This is wrapper around the 'mapshaper' 'JavaScript' library by Matthew Bloch <https://github.com/mbloch/mapshaper/> to perform topologically-aware polygon simplification, as well as other operations such as clipping, erasing, dissolving, and converting 'multi-part' to 'single-part' geometries.

Maintained by Andy Teucher. Last updated 9 months ago.

rlang

204 stars 11.64 score 2.1k scripts 18 dependents

jthomasmock

gtExtras:Extending 'gt' for Beautiful HTML Tables

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

Maintained by Thomas Mock. Last updated 12 months ago.

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

199 stars 11.45 score 2.4k scripts 3 dependents

ropensci

EML:Read and Write Ecological Metadata Language Files

Work with Ecological Metadata Language ('EML') files. 'EML' is a widely used metadata standard in the ecological and environmental sciences, described in Jones et al. (2006), <doi:10.1146/annurev.ecolsys.37.091305.110031>.

Maintained by Carl Boettiger. Last updated 3 years ago.

eml eml-metadata metadata-standard

97 stars 11.19 score 378 scripts 7 dependents

ropensci

geojsonio:Convert Data from and to 'GeoJSON' or 'TopoJSON'

Convert data to 'GeoJSON' or 'TopoJSON' from various R classes, including vectors, lists, data frames, shape files, and spatial classes. 'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos', but rather aims to be a high level client to simplify conversions of data from and to 'GeoJSON' and 'TopoJSON'.

Maintained by Michael Mahoney. Last updated 1 years ago.

geojson topojson geospatial conversion data input-output io

151 stars 10.83 score 2.9k scripts 13 dependents

rstudio

pointblank:Data Validation and Organization of Metadata for Local and Remote Tables

Validate data in data frames, 'tibble' objects, 'Spark' 'DataFrames', and database tables. Validation pipelines can be made using easily-readable, consecutive validation steps. Upon execution of the validation plan, several reporting options are available. User-defined thresholds for failure rates allow for the determination of appropriate reporting actions. Many other workflows are available including an information management workflow, where the aim is to record, collect, and generate useful information on data tables.

Maintained by Richard Iannone. Last updated 3 days ago.

data-assertions data-checker data-dictionaries data-frames data-inference data-management data-profiler data-quality data-validation data-verification database-tables easy-to-understand reporting-tool schema-validation testing-tools yaml-configuration

942 stars 10.73 score 284 scripts

business-science

modeltime:The Tidymodels Extension for Time Series Modeling

The time series forecasting framework for use with the 'tidymodels' ecosystem. Models include ARIMA, Exponential Smoothing, and additional time series models from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition" (<https://otexts.com/fpp2/>). Refer to "Prophet: forecasting at scale" (<https://research.facebook.com/blog/2017/02/prophet-forecasting-at-scale/>.).

Maintained by Matt Dancho. Last updated 5 months ago.

arima data-science deep-learning ets forecasting machine-learning machine-learning-algorithms modeltime prophet tbats tidymodeling tidymodels time time-series time-series-analysis timeseries timeseries-forecasting

551 stars 10.61 score 1.1k scripts 7 dependents

ropensci

jsonvalidate:Validate 'JSON' Schema

Uses the node library 'is-my-json-valid' or 'ajv' to validate 'JSON' against a 'JSON' schema. Drafts 04, 06 and 07 of 'JSON' schema are supported.

Maintained by Rich FitzJohn. Last updated 2 months ago.

json json-validation jsonvalidate

49 stars 10.54 score 29 scripts 45 dependents

bioc

singleCellTK:Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.

Maintained by Joshua David Campbell. Last updated 1 months ago.

singlecell geneexpression differentialexpression alignment clustering immunooncology batcheffect normalization qualitycontrol dataimport gui

182 stars 10.17 score 252 scripts

ropensci

cffr:Generate Citation File Format ('cff') Metadata for R Packages

The Citation File Format version 1.2.0 <doi:10.5281/zenodo.5171937> is a human and machine readable file format which provides citation metadata for software. This package provides core utilities to generate and validate this metadata.

Maintained by Diego Hernangómez. Last updated 6 days ago.

attribution citation credit citation-files cff metadata citation-file-format ropensci

25 stars 9.69 score 116 scripts 3 dependents

rich-iannone

DiagrammeRsvg:Export DiagrammeR Graphviz Graphs as SVG

Allows for export of DiagrammeR Graphviz objects to SVG.

Maintained by Richard Iannone. Last updated 5 years ago.

29 stars 9.56 score 462 scripts 18 dependents

cbielow

PTXQC:Quality Report Generation for MaxQuant and mzTab Results

Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.

Maintained by Chris Bielow. Last updated 1 years ago.

drag-and-drop hacktoberfest heatmap match-between-runs maxquant metric mztab openms proteomics quality-control quality-metrics report

42 stars 9.35 score 105 scripts 1 dependents

microsoft

finnts:Microsoft Finance Time Series Forecasting Framework

Automated time series forecasting developed by Microsoft Finance. The Microsoft Finance Time Series Forecasting Framework, aka Finn, can be used to forecast any component of the income statement, balance sheet, or any other area of interest by finance. Any numerical quantity over time, Finn can be used to forecast it. While it can be applied outside of the finance domain, Finn was built to meet the needs of financial analysts to better forecast their businesses within a company, and has a lot of built in features that are specific to the needs of financial forecasters. Happy forecasting!

Maintained by Mike Tokic. Last updated 1 months ago.

business data-science feature-selection finance finnts forecasting machine-learning microsoft time-series

194 stars 9.30 score 39 scripts

joelgombin

concaveman:A Very Fast 2D Concave Hull Algorithm

The concaveman function ports the 'concaveman' (<https://github.com/mapbox/concaveman>) library from 'mapbox'. It computes the concave polygon(s) for one or several set of points.

Maintained by Joël Gombin. Last updated 3 years ago.

concave-hull spatial

66 stars 9.06 score 492 scripts 22 dependents

bioc

schex:Hexbin plots for single cell omics data

Builds hexbin plots for variables and dimension reduction stored in single cell omics data such as SingleCellExperiment. The ideas used in this package are based on the excellent work of Dan Carr, Nicholas Lewin-Koh, Martin Maechler and Thomas Lumley.

Maintained by Saskia Freytag. Last updated 5 months ago.

software sequencing singlecell dimensionreduction visualization immunooncology dataimport

74 stars 8.96 score 102 scripts 2 dependents

merck

gsDesign2:Group Sequential Design with Non-Constant Effect

The goal of 'gsDesign2' is to enable fixed or group sequential design under non-proportional hazards. To enable highly flexible enrollment, time-to-event and time-to-dropout assumptions, 'gsDesign2' offers piecewise constant enrollment, failure rates, and dropout rates for a stratified population. This package includes three methods for designs: average hazard ratio, weighted logrank tests in Yung and Liu (2019) <doi:10.1111/biom.13196>, and MaxCombo tests. Substantial flexibility on top of what is in the 'gsDesign' package is intended for selecting boundaries.

Maintained by Yujie Zhao. Last updated 19 hours ago.

cpp

22 stars 8.91 score 186 scripts

jeroen

js:Tools for Working with JavaScript in R

A set of utilities for working with JavaScript syntax in R. Includes tools to parse, tokenize, compile, validate, reformat, optimize and analyze JavaScript code.

Maintained by Jeroen Ooms. Last updated 6 months ago.

68 stars 8.87 score 83 scripts 1 dependents

terminological

dtrackr:Track your Data Pipelines

Track and document 'dplyr' data pipelines. As you filter, mutate, and join your way through a data set, 'dtrackr' seamlessly keeps track of your data flow and makes publication ready documentation of a data pipeline simple.

Maintained by Robert Challen. Last updated 5 months ago.

69 stars 8.78 score 362 scripts 1 dependents

palaeoverse

palaeoverse:Prepare and Explore Data for Palaeobiological Analyses

Provides functionality to support data preparation and exploration for palaeobiological analyses, improving code reproducibility and accessibility. The wider aim of 'palaeoverse' is to bring the palaeobiological community together to establish agreed standards. The package currently includes functionality for data cleaning, binning (time and space), exploration, summarisation and visualisation. Reference datasets (i.e. Geological Time Scales <https://stratigraphy.org/chart>) and auxiliary functions are also provided. Details can be found in: Jones et al., (2023) <doi: 10.1111/2041-210X.14099>.

Maintained by Lewis A. Jones. Last updated 5 months ago.

biodiversity fossil palaeobiology paleobiology

21 stars 8.51 score 44 scripts 1 dependents

bioc

alabaster.base:Save Bioconductor Objects to File

Save Bioconductor data structures into file artifacts, and load them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Maintained by Aaron Lun. Last updated 24 days ago.

datarepresentation dataimport zlib cpp

3 stars 8.47 score 60 scripts 15 dependents

davisvaughan

almanac:Tools for Working with Recurrence Rules

Provides tools for defining recurrence rules and recurrence sets. Recurrence rules are a programmatic way to define a recurring event, like the first Monday of December. Multiple recurrence rules can be combined into larger recurrence sets. A full holiday and calendar interface is also provided that can generate holidays within a particular year, can detect if a date is a holiday, can respect holiday observance rules, and allows for custom holidays.

Maintained by Davis Vaughan. Last updated 2 years ago.

calendars holidays recurrence-rules

73 stars 8.40 score 65 scripts 1 dependents

obrl-soil

h3jsr:Access Uber's H3 Library

Provides access to Uber's H3 library for geospatial indexing via its JavaScript transpile 'h3-js' <https://github.com/uber/h3-js> and 'V8' <https://github.com/jeroen/v8>.

Maintained by Lauren OBrien. Last updated 1 years ago.

discrete-global-grids h3 spatial-indexing

67 stars 8.39 score 205 scripts 4 dependents

ropensci

nodbi:'NoSQL' Database Connector

Simplified JSON document database access and manipulation, providing a common API across supported 'NoSQL' databases 'Elasticsearch', 'CouchDB', 'MongoDB' as well as 'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.

Maintained by Ralf Herold. Last updated 5 months ago.

database mongodb elasticsearch couchdb sqlite postgresql duckdb nosql json documents

78 stars 8.36 score 28 scripts 1 dependents

business-science

modeltime.ensemble:Ensemble Algorithms for Time Series Forecasting with Modeltime

A 'modeltime' extension that implements time series ensemble forecasting methods including model averaging, weighted averaging, and stacking. These techniques are popular methods to improve forecast accuracy and stability.

Maintained by Matt Dancho. Last updated 8 months ago.

ensemble ensemble-learning forecast forecasting modeltime stacking stacking-ensemble tidymodels time time-series timeseries

77 stars 8.30 score 143 scripts

nceas

metajam:Easily Download Data and Metadata from 'DataONE'

A set of tools to foster the development of reproducible analytical workflow by simplifying the download of data and metadata from 'DataONE' (<https://www.dataone.org>) and easily importing this information into R.

Maintained by Julien Brun. Last updated 7 months ago.

data data-analysis metadata repositories

16 stars 8.21 score 75 scripts

ropensci

katex:Rendering Math to HTML, 'MathML', or R-Documentation Format

Convert latex math expressions to HTML and 'MathML' for use in markdown documents or package manual pages. The rendering is done in R using the V8 engine (i.e. server-side), which eliminates the need for embedding the 'MathJax' library into your web pages. In addition a 'math-to-rd' wrapper is provided to automatically render beautiful math in R documentation files.

Maintained by Jeroen Ooms. Last updated 6 months ago.

37 stars 8.16 score 29 scripts 6 dependents

mazamascience

MazamaSpatialUtils:Spatial Data Download and Utility Functions

A suite of conversion functions to create internally standardized spatial polygons data frames. Utility functions use these data sets to return values such as country, state, time zone, watershed, etc. associated with a set of longitude/latitude pairs. (They also make cool maps.)

Maintained by Jonathan Callahan. Last updated 5 months ago.

5 stars 8.09 score 282 scripts 2 dependents

rstudio

juicyjuice:Inline CSS Properties into HTML Tags Using 'juice'

There are occasions where you need a piece of HTML with integrated styles. A prime example of this is HTML email. This transformation involves moving the CSS and associated formatting instructions from the style block in the head of your document into the body of the HTML. Many prominent email clients require integrated styles in HTML email; otherwise a received HTML email will be displayed without any styling. This package will quickly and precisely perform these CSS transformations when given HTML text and it does so by using the JavaScript 'juice' library.

Maintained by Richard Iannone. Last updated 1 years ago.

css html inlining

3 stars 8.07 score 1 scripts 115 dependents

ropensci

MODIStsp:Find, Download and Process MODIS Land Products Data

Allows automating the creation of time series of rasters derived from MODIS satellite land products data. It performs several typical preprocessing steps such as download, mosaicking, reprojecting and resizing data acquired on a specified time period. All processing parameters can be set using a user-friendly GUI. Users can select which layers of the original MODIS HDF files they want to process, which additional quality indicators should be extracted from aggregated MODIS quality assurance layers and, in the case of surface reflectance products, which spectral indexes should be computed from the original reflectance bands. For each output layer, outputs are saved as single-band raster files corresponding to each available acquisition date. Virtual files allowing access to the entire time series as a single file are also created. Command-line execution exploiting a previously saved processing options file is also possible, allowing users to automatically update time series related to a MODIS product whenever a new image is available. For additional documentation refer to the following article: Busetto and Ranghetti (2016) <doi:10.1016/j.cageo.2016.08.020>.

Maintained by Luigi Ranghetti. Last updated 8 months ago.

gdal modis modis-data modis-land-products peer-reviewed preprocessing remote-sensing satellite-imagery time-series

156 stars 8.04 score 86 scripts 1 dependents

gsk-biostatistics

tfrmt:Applies Display Metadata to Analysis Results Datasets

Creates a framework to store and apply display metadata to Analysis Results Datasets (ARDs). The use of 'tfrmt' allows users to define table format and styling without the data, and later apply the format to the data.

Maintained by Becca Krouse. Last updated 4 months ago.

73 stars 8.03 score 84 scripts 1 dependents

bioc

spicyR:Spatial analysis of in situ cytometry data

The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.

Maintained by Ellis Patrick. Last updated 25 days ago.

singlecell cellbasedassays spatial

9 stars 8.02 score 57 scripts 1 dependents

rfhb

ctrdata:Retrieve and Analyze Clinical Trials Data from Public Registers

A system for querying, retrieving and analyzing protocol- and results-related information on clinical trials from four public registers, the 'European Union Clinical Trials Register' ('EUCTR', <https://www.clinicaltrialsregister.eu/>), 'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also translating queries the retired classic interface), the 'ISRCTN' (<http://www.isrctn.com/>) and the 'European Union Clinical Trials Information System' ('CTIS', <https://euclinicaltrials.eu/>). Trial information is downloaded, converted and stored in a database ('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi'). Protocols, statistical analysis plans, informed consent sheets and other documents in registers associated with trials can also be downloaded. Other functions implement trial concepts canonically across registers, identify deduplicated records, easily find and extract variables (fields) of interest even from complex nested data as used by the registers, merge variables and update queries. The package can be used for monitoring, meta- and trend-analysis of the design and conduct as well as of the results of clinical trials across registers.

Maintained by Ralf Herold. Last updated 8 days ago.

clinical-data clinical-research clinical-studies clinical-trials ctgov database duckdb mongodb nodbi postgresql register sqlite studies trial

45 stars 7.97 score 32 scripts

mthulin

boot.pval:Bootstrap p-Values

Computation of bootstrap p-values through inversion of confidence intervals, including convenience functions for regression models and tests of location.

Maintained by Måns Thulin. Last updated 23 days ago.

bootstrap p-value regression-models

4 stars 7.89 score 36 scripts 3 dependents

giscience

openrouteservice:An 'openrouteservice' API Client

The client streamlines access to the services provided by <https://api.openrouteservice.org>. It allows you to painlessly query for directions, isochrones, time-distance matrices, geocoding, elevation, points of interest, and more.

Maintained by Andrzej K. Oleś. Last updated 2 months ago.

api directions gis giscience isochrones openrouteservice openstreetmap pois routing sdk

108 stars 7.89 score 60 scripts

tysonstanley

furniture:Furniture for Quantitative Scientists

Contains four main functions (i.e., four pieces of furniture): table1() which produces a well-formatted table of descriptive statistics common as Table 1 in research articles, tableC() which produces a well-formatted table of correlations, tableF() which provides frequency counts, and washer() which is helpful in cleaning up the data. These furniture-themed functions are designed to simplify common tasks in quantitative analysis. Other data summary and cleaning tools are also available.

Maintained by Tyson S. Barrett. Last updated 1 years ago.

descriptive-statistics exploratory-data-analysis health table-one table1 tables tidy tidyverse

50 stars 7.89 score 256 scripts 1 dependents

ediorg

ecocomDP:Tools to Create, Use, and Convert ecocomDP Data

Work with the Ecological Community Data Design Pattern. 'ecocomDP' is a flexible data model for harmonizing ecological community surveys, in a research question agnostic format, from source data published across repositories, and with methods that keep the derived data up-to-date as the underlying sources change. Described in O'Brien et al. (2021), <doi:10.1016/j.ecoinf.2021.101374>.

Maintained by Colin Smith. Last updated 8 months ago.

32 stars 7.74 score 77 scripts

mrc-ide

naomi:Naomi Model for Subnational HIV Estimates

This package implements the Naomi model for subnational HIV estimates.

Maintained by Jeff Eaton. Last updated 19 days ago.

cpp

9 stars 7.74 score 54 scripts 2 dependents

ropensci

emld:Ecological Metadata as Linked Data

This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.

Maintained by Carl Boettiger. Last updated 4 years ago.

13 stars 7.63 score 69 scripts 8 dependents

spsanderson

healthyR.ts:The Time Series Modeling Companion to 'healthyR'

Hospital time series data analysis workflow tools, modeling, and automations. This library provides many useful tools to review common administrative time series hospital data. Some of these include average length of stay, and readmission rates. The aim is to provide a simple and consistent verb framework that takes the guesswork out of everything.

Maintained by Steven Sanderson. Last updated 6 months ago.

ai arima-forecasting arima-model ets forecasting ggplot2 machine-learning modeling prophet time-series time-series-analysis workflows

19 stars 7.58 score 56 scripts 1 dependents

bioc

imcRtools:Methods for imaging mass cytometry data analysis

This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.

Maintained by Daniel Schulz. Last updated 5 months ago.

immunooncology singlecell spatial dataimport clustering imc single-cell

24 stars 7.58 score 126 scripts

sem-in-r

seminr:Building and Estimating Structural Equation Models

A powerful, easy to syntax for specifying and estimating complex Structural Equation Models. Models can be estimated using Partial Least Squares Path Modeling or Covariance-Based Structural Equation Modeling or covariance based Confirmatory Factor Analysis. Methods described in Ray, Danks, and Valdez (2021).

Maintained by Nicholas Patrick Danks. Last updated 3 years ago.

common-factors composites construct pls-models

62 stars 7.46 score 284 scripts

ropensci

dataspice:Create Lightweight Schema.org Descriptions of Data

The goal of 'dataspice' is to make it easier for researchers to create basic, lightweight, and concise metadata files for their datasets. These basic files can then be used to make useful information available during analysis, create a helpful dataset "README" webpage, and produce more complex metadata formats to aid dataset discovery. Metadata fields are based on the 'Schema.org' and 'Ecological Metadata Language' standards.

Maintained by Bryce Mecum. Last updated 4 years ago.

data dataset metadata schema-org unconf unconf18

162 stars 7.45 score 25 scripts

bioc

gDRutils:A package with helper functions for processing drug response data

This package contains utility functions used throughout the gDR platform to fit data, manipulate data, and convert and validate data structures. This package also has the necessary default constants for gDR platform. Many of the functions are utilized by the gDRcore package.

Maintained by Arkadiusz Gladki. Last updated 2 days ago.

software infrastructure

2 stars 7.42 score 3 scripts 3 dependents

bioc

igvShiny:igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

This package is a wrapper of Integrative Genomics Viewer (IGV). It comprises an htmlwidget version of IGV. It can be used as a module in Shiny apps.

Maintained by Arkadiusz Gladki. Last updated 5 months ago.

software shinyapps sequencing coverage

37 stars 7.40 score 120 scripts

spsanderson

healthyR.ai:The Machine Learning and AI Modeling Companion to 'healthyR'

Hospital machine learning and ai data analysis workflow tools, modeling, and automations. This library provides many useful tools to review common administrative hospital data. Some of these include predicting length of stay, and readmits. The aim is to provide a simple and consistent verb framework that takes the guesswork out of everything.

Maintained by Steven Sanderson. Last updated 2 months ago.

ai artificial-intelligence healthcareanalytics healthyr healthyverse machine-learning

16 stars 7.37 score 36 scripts 1 dependents

bioc

gDRimport:Package for handling the import of dose-response data

The package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose-response data provided in different file formats.

Maintained by Arkadiusz Gladki. Last updated 2 days ago.

software infrastructure dataimport

3 stars 7.32 score 5 scripts 1 dependents

bioc

gDRcore:Processing functions and interface to process and analyze drug dose-response data

This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the pipeline function allowing analyzing the data in a straightforward way.

Maintained by Arkadiusz Gladki. Last updated 17 days ago.

software shinyapps cpp

2 stars 7.25 score 4 scripts 1 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 4 days ago.

nfl nflfastr nflstats nflverse sports-analytics sportsanalytics

19 stars 7.21 score 316 scripts 1 dependents

cardiomoon

autoReg:Automatic Linear and Logistic Regression and Survival Analysis

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

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

49 stars 7.13 score 69 scripts

openanalytics

clinDataReview:Clinical Data Review Tool

Creation of interactive tables, listings and figures ('TLFs') and associated report for exploratory analysis of data in a clinical trial, e.g. for clinical oversight activities. Interactive figures include sunburst, treemap, scatterplot, line plot and barplot of counts data. Interactive tables include table of summary statistics (as counts of adverse events, enrollment table) and listings. Possibility to compare data (summary table or listing) across two data batches/sets. A clinical data review report is created via study-specific configuration files and template 'R Markdown' reports contained in the package.

Maintained by Laure Cougnaud. Last updated 10 months ago.

11 stars 7.10 score 36 scripts

nbarrowman

vtree:Display Information About Nested Subsets of a Data Frame

A tool for calculating and drawing "variable trees". Variable trees display information about nested subsets of a data frame.

Maintained by Nick Barrowman. Last updated 14 days ago.

data-science data-visualization exploratory-data-analysis statistics

76 stars 7.09 score 65 scripts

mskcc-epi-bio

tidycmprsk:Competing Risks Estimation

Provides an intuitive interface for working with the competing risk endpoints. The package wraps the 'cmprsk' package, and exports functions for univariate cumulative incidence estimates and competing risk regression. Methods follow those introduced in Fine and Gray (1999) <doi:10.1002/sim.7501>.

Maintained by Daniel D. Sjoberg. Last updated 7 months ago.

competing-risks

23 stars 7.06 score 157 scripts 1 dependents

ropensci

jsonld:JSON for Linking Data

JSON-LD <https://www.w3.org/TR/json-ld/> is a light-weight syntax for expressing linked data. It is primarily intended for web-based programming environments, interoperable web services and for storing linked data in JSON-based databases. This package provides bindings to the JavaScript library for converting, expanding and compacting JSON-LD documents.

Maintained by Jeroen Ooms. Last updated 6 months ago.

json-ld

35 stars 7.05 score 74 scripts 11 dependents

bioc

alabaster.matrix:Load and Save Artifacts from File

Save matrices, arrays and similar objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Maintained by Aaron Lun. Last updated 24 days ago.

dataimport datarepresentation cpp

7.05 score 15 scripts 8 dependents

bioc

sechm:sechm: Complex Heatmaps from a SummarizedExperiment

sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible. These functionalities used to be part of the SEtools package.

Maintained by Pierre-Luc Germain. Last updated 1 months ago.

geneexpression visualization

6 stars 7.03 score 60 scripts 2 dependents

bioc

pipeComp:pipeComp pipeline benchmarking framework

A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.

Maintained by Pierre-Luc Germain. Last updated 5 months ago.

geneexpression transcriptomics clustering datarepresentation benchmark bioconductor pipeline-benchmarking pipelines single-cell-rna-seq

41 stars 7.02 score 43 scripts

edwindj

daff:Diff, Patch and Merge for Data.frames

Diff, patch and merge for data frames. Document changes in data sets and use them to apply patches. Changes to data can be made visible by using render_diff(). The 'V8' package is used to wrap the 'daff.js' 'JavaScript' library which is included in the package.

Maintained by Edwin de Jonge. Last updated 1 years ago.

daff data diff

152 stars 6.99 score 133 scripts

shannonpileggi

gtreg:Regulatory Tables for Clinical Research

Creates tables suitable for regulatory agency submission by leveraging the 'gtsummary' package as the back end. Tables can be exported to HTML, Word, PDF and more. Highly customized outputs are available by utilizing existing styling functions from 'gtsummary' as well as custom options designed for regulatory tables.

Maintained by Shannon Pileggi. Last updated 1 months ago.

37 stars 6.92 score 30 scripts

ips-lmu

emuR:Main Package of the EMU Speech Database Management System

Provide the EMU Speech Database Management System (EMU-SDMS) with database management, data extraction, data preparation and data visualization facilities. See <https://ips-lmu.github.io/The-EMU-SDMS-Manual/> for more details.

Maintained by Markus Jochim. Last updated 1 years ago.

24 stars 6.89 score 135 scripts 1 dependents

biogen-inc

tidyCDISC:Quick Table Generation & Exploratory Analyses on ADaM-Ish Datasets

Provides users a quick exploratory dive into common visualizations without writing a single line of code given the users data follows the Analysis Data Model (ADaM) standards put forth by the Clinical Data Interchange Standards Consortium (CDISC) <https://www.cdisc.org>. Prominent modules/ features of the application are the Table Generator, Population Explorer, and the Individual Explorer. The Table Generator allows users to drag and drop variables and desired statistics (frequencies, means, ANOVA, t-test, and other summary statistics) into bins that automagically create stunning tables with validated information. The Population Explorer offers various plots to visualize general trends in the population from various vantage points. Plot modules currently include scatter plot, spaghetti plot, box plot, histogram, means plot, and bar plot. Each plot type allows the user to plot uploaded variables against one another, and dissect the population by filtering out certain subjects. Last, the Individual Explorer establishes a cohesive patient narrative, allowing the user to interact with patient metrics (params) by visit or plotting important patient events on a timeline. All modules allow for concise filtering & downloading bulk outputs into html or pdf formats to save for later.

Maintained by Aaron Clark. Last updated 2 years ago.

pharma rinpharma

108 stars 6.86 score 19 scripts

raymondbalise

rUM:R Templates from the University of Miami

This holds some r markdown and quarto templates and a template to create a research project in "R Studio".

Maintained by Raymond Balise. Last updated 8 days ago.

rmarkdown

9 stars 6.84 score 16 scripts

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 5 days ago.

13 stars 6.83 score 9 scripts

rte-antares-rpackage

antaresViz:Antares Visualizations

Visualize results generated by Antares, a powerful open source software developed by RTE to simulate and study electric power systems (more information about 'Antares' here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). This package provides functions that create interactive charts to help 'Antares' users visually explore the results of their simulations.

Maintained by Tatiana Vargas. Last updated 3 months ago.

adequacy bilan dygraphs electric energy leaflet linear-programming manipulatewidge monte-carlo-simulation optimization plotly previsionnel renewable-energy rte shiny shiny-apps simulation stochastic-simulation-algorithm tyndp

21 stars 6.83 score 32 scripts

harrison4192

autostats:Auto Stats

Automatically do statistical exploration. Create formulas using 'tidyselect' syntax, and then determine cross-validated model accuracy and variable contributions using 'glm' and 'xgboost'. Contains additional helper functions to create and modify formulas. Has a flagship function to quickly determine relationships between categorical and continuous variables in the data set.

Maintained by Harrison Tietze. Last updated 24 days ago.

6 stars 6.76 score 5 scripts 2 dependents

frbcesab

rcompendium:Create a Package or Research Compendium Structure

Makes easier the creation of R package or research compendium (i.e. a predefined files/folders structure) so that users can focus on the code/analysis instead of wasting time organizing files. A full ready-to-work structure is set up with some additional features: version control, remote repository creation, CI/CD configuration (check package integrity under several OS, test code with 'testthat', and build and deploy website using 'pkgdown'). This package heavily relies on the R packages 'devtools' and 'usethis' and follows recommendations made by Wickham H. (2015) <ISBN:9781491910597> and Marwick B. et al. (2018) <doi:10.7287/peerj.preprints.3192v2>.

Maintained by Nicolas Casajus. Last updated 2 months ago.

reproducible-research research-compendium

40 stars 6.72 score 22 scripts

harrison4192

presenter:Present Data with Style

Consists of custom wrapper functions using packages 'openxlsx', 'flextable', and 'officer' to create highly formatted MS office friendly output of your data frames. These viewer friendly outputs are intended to match expectations of professional looking presentations in business and consulting scenarios. The functions are opinionated in the sense that they expect the input data frame to have certain properties in order to take advantage of the automated formatting.

Maintained by Harrison Tietze. Last updated 2 years ago.

excel powerpoint

11 stars 6.69 score 15 scripts 4 dependents

bioc

epiregulon:Gene regulatory network inference from single cell epigenomic data

Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.

Maintained by Xiaosai Yao. Last updated 19 days ago.

singlecell generegulation networkinference network geneexpression transcription genetarget cpp

14 stars 6.67 score 17 scripts

business-science

modeltime.resample:Resampling Tools for Time Series Forecasting

A 'modeltime' extension that implements forecast resampling tools that assess time-based model performance and stability for a single time series, panel data, and cross-sectional time series analysis.

Maintained by Matt Dancho. Last updated 1 years ago.

accuracy-metrics backtesting bootstrap bootstrapping cross-validation forecasting modeltime modeltime-resample resampling statistics tidymodels time-series

19 stars 6.64 score 38 scripts 1 dependents

bioc

lisaClust:lisaClust: Clustering of Local Indicators of Spatial Association

lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.

Maintained by Ellis Patrick. Last updated 4 months ago.

singlecell cellbasedassays spatial

3 stars 6.64 score 48 scripts

atusy

minidown:Create Simple Yet Powerful HTML Documents with Light Weight CSS Frameworks

Create minimal, responsive, and style-agnostic HTML documents with the lightweight CSS frameworks such as 'sakura', 'Water.css', and 'spcss'. Powerful features include table of contents floating as a sidebar, folding codes and results, and more.

Maintained by Atsushi Yasumoto. Last updated 3 years ago.

79 stars 6.55 score 15 scripts 1 dependents

taxonomicallyinformedannotation

tima:Taxonomically Informed Metabolite Annotation

This package provides the infrastructure to perform Taxonomically Informed Metabolite Annotation.

Maintained by Adriano Rutz. Last updated 4 hours ago.

metabolite annotation chemotaxonomy scoring system natural products computational metabolomics taxonomic distance specialized metabolome

9 stars 6.55 score 32 scripts 2 dependents

srkobakian

sugarbag:Create Tessellated Hexagon Maps

Create a hexagon tile map display from spatial polygons. Each polygon is represented by a hexagon tile, placed as close to it's original centroid as possible, with a focus on maintaining spatial relationship to a focal point. Developed to aid visualisation and analysis of spatial distributions across Australia, which can be challenging due to the concentration of the population on the coast and wide open interior.

Maintained by Dianne Cook. Last updated 2 years ago.

42 stars 6.52 score 53 scripts

bioc

Statial:A package to identify changes in cell state relative to spatial associations

Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.

Maintained by Farhan Ameen. Last updated 5 months ago.

singlecell spatial classification single-cell

5 stars 6.49 score 23 scripts

dhaine

episensr:Basic Sensitivity Analysis of Epidemiological Results

Basic sensitivity analysis of the observed relative risks adjusting for unmeasured confounding and misclassification of the exposure/outcome, or both. It follows the bias analysis methods and examples from the book by Lash T.L, Fox M.P, and Fink A.K. "Applying Quantitative Bias Analysis to Epidemiologic Data", ('Springer', 2021).

Maintained by Denis Haine. Last updated 1 years ago.

bias epidemiology sensitivity-analysis statistics

13 stars 6.48 score 39 scripts 1 dependents

gisma

uavRmp:UAV Mission Planner

The Unmanned Aerial Vehicle Mission Planner provides an easy to use work flow for planning autonomous obstacle avoiding surveys of ready to fly unmanned aerial vehicles to retrieve aerial or spot related data. It creates either intermediate flight control files for the DJI-Litchi supported series or ready to upload control files for the pixhawk-based flight controller as used in the 3DR-Solo or Yuneec series. Additionally it contains some useful tools for digitizing and data manipulation.

Maintained by Chris Reudenbach. Last updated 10 months ago.

cultural-heritage dji drone flight-planning forest-mapping litchi low-budget-uav mission-planning photogrammetry pixhawk pixhawk-controller qgroundcontrol2litchi solo survey terrain-following terrain-mapping uavs yuneec

25 stars 6.48 score 6 scripts

jazznbass

scan:Single-Case Data Analyses for Single and Multiple Baseline Designs

A collection of procedures for analysing, visualising, and managing single-case data. These include piecewise linear regression models, multilevel models, overlap indices ('PND', 'PEM', 'PAND', 'PET', 'tau-u', 'baseline corrected tau', 'CDC'), and randomization tests. Data preparation functions support outlier detection, handling missing values, scaling, and custom transformations. An export function helps to generate html, word, and latex tables in a publication friendly style. More details can be found in the online book 'Analyzing single-case data with R and scan', Juergen Wilbert (2025) <https://jazznbass.github.io/scan-Book/>.

Maintained by Juergen Wilbert. Last updated 10 days ago.

4 stars 6.47 score 62 scripts 1 dependents

hugomflavio

actel:Acoustic Telemetry Data Analysis

Designed for studies where animals tagged with acoustic tags are expected to move through receiver arrays. This package combines the advantages of automatic sorting and checking of animal movements with the possibility for user intervention on tags that deviate from expected behaviour. The three analysis functions (explore(), migration() and residency()) allow the users to analyse their data in a systematic way, making it easy to compare results from different studies. CJS calculations are based on Perry et al. (2012) <https://www.researchgate.net/publication/256443823_Using_mark-recapture_models_to_estimate_survival_from_telemetry_data>.

Maintained by Hugo Flávio. Last updated 1 months ago.

acoustic-telemetry fish-packages telemetry-data

26 stars 6.46 score 16 scripts

bioc

alabaster.se:Load and Save SummarizedExperiments from File

Save SummarizedExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Maintained by Aaron Lun. Last updated 5 months ago.

dataimport datarepresentation

6.39 score 8 scripts 7 dependents

tarakc02

rmapzen:Client for 'Mapzen' and Related Map APIs

Provides an interface to 'Mapzen'-based APIs (including geocode.earth, Nextzen, and NYC GeoSearch) for geographic search and geocoding, isochrone calculation, and vector data to draw map tiles. See <https://www.mapzen.com/documentation/> for more information. The original Mapzen has gone out of business, but 'rmapzen' can be set up to work with any provider who implements the Mapzen API.

Maintained by Tarak Shah. Last updated 1 years ago.

34 stars 6.39 score 72 scripts

mattheaphy

actxps:Create Actuarial Experience Studies: Prepare Data, Summarize Results, and Create Reports

Experience studies are used by actuaries to explore historical experience across blocks of business and to inform assumption setting activities. This package provides functions for preparing data, creating studies, visualizing results, and beginning assumption development. Experience study methods, including exposure calculations, are described in: Atkinson & McGarry (2016) "Experience Study Calculations" <https://www.soa.org/49378a/globalassets/assets/files/research/experience-study-calculations.pdf>. The limited fluctuation credibility method used by the 'exp_stats()' function is described in: Herzog (1999, ISBN:1-56698-374-6) "Introduction to Credibility Theory".

Maintained by Matt Heaphy. Last updated 3 months ago.

14 stars 6.38 score 23 scripts

bioc

alabaster.ranges:Load and Save Ranges-related Artifacts from File

Save GenomicRanges, IRanges and related data structures into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Maintained by Aaron Lun. Last updated 5 months ago.

dataimport datarepresentation

6.38 score 8 scripts 8 dependents

r-lib

asciicast:Create 'Ascii' Screen Casts from R Scripts

Record 'asciicast' screen casts from R scripts. Convert them to animated SVG images, to be used in 'README' files, or blog posts. Includes 'asciinema-player' as an 'HTML' widget, and an 'asciicast' 'knitr' engine, to embed 'ascii' screen casts in 'Rmarkdown' documents.

Maintained by Gábor Csárdi. Last updated 6 months ago.

232 stars 6.34 score 8 scripts

inbo

camtraptor:Read, Explore and Visualize Camera Trap Data Packages

Read, explore and visualize Camera Trap Data Packages (Camtrap DP). 'Camtrap DP' (<https://camtrap-dp.tdwg.org>) is a community developed data exchange format for this type of data. With camtraptor you can read and filter data, create overviews of observed species, relative abundance or effort, and plot these data on a map.

Maintained by Damiano Oldoni. Last updated 1 months ago.

camera-traps oscibio

12 stars 6.27 score 16 scripts

ropensci

deposits:A universal client for depositing and accessing research data anywhere

A universal client for depositing and accessing research data anywhere. Currently supported services are zenodo and figshare.

Maintained by Mark Padgham. Last updated 7 months ago.

39 stars 6.21 score 8 scripts 2 dependents

pachadotdev

chilemapas:Mapas de las Divisiones Politicas y Administrativas de Chile (Maps of the Political and Administrative Divisions of Chile)

Mapas terrestres con topologias simplificadas. Estos mapas no tienen precision geodesica, por lo que aplica el DFL-83 de 1979 de la Republica de Chile y se consideran referenciales sin validez legal. No se incluyen los territorios antarticos y bajo ningun evento estos mapas significan que exista una cesion u ocupacion de territorios soberanos en contra del Derecho Internacional por parte de Chile. Esta paquete esta documentado intencionalmente en castellano asciificado para que funcione sin problema en diferentes plataformas. (Terrestrial maps with simplified toplogies. These maps lack geodesic precision, therefore DFL-83 1979 of the Republic of Chile applies and are considered to have no legal validity. Antartic territories are excluded and under no event these maps mean there is a cession or occupation of sovereign territories against International Laws from Chile. This package was intentionally documented in asciified spanish to make it work without problem on different platforms.)

Maintained by Mauricio Vargas. Last updated 3 years ago.

chile geojson maps tidyverse topojson

35 stars 6.21 score 93 scripts

ms-quality-hub

rmzqc:Creation, Reading and Validation of 'mzqc' Files

Reads, writes and validates 'mzQC' files. The 'mzQC' format is a standardized file format for the exchange, transmission, and archiving of quality metrics derived from biological mass spectrometry data, as defined by the HUPO-PSI (Human Proteome Organisation - Proteomics Standards Initiative) Quality Control working group. See <https://hupo-psi.github.io/mzQC/> for details.

Maintained by Chris Bielow. Last updated 22 hours ago.

hacktoberfest mass-spectrometry mzqc quality-control

3 stars 6.21 score 10 scripts 3 dependents

matildabrown

rWCVP:Generating Summaries, Reports and Plots from the World Checklist of Vascular Plants

A companion to the World Checklist of Vascular Plants (WCVP). It includes functions to generate maps and species lists, as well as match names to the WCVP. For more details and to cite the package, see: Brown M.J.M., Walker B.E., Black N., Govaerts R., Ondo I., Turner R., Nic Lughadha E. (in press). "rWCVP: A companion R package to the World Checklist of Vascular Plants". New Phytologist.

Maintained by Matilda Brown. Last updated 1 years ago.

22 stars 6.17 score 45 scripts 1 dependents

ohdsi

OmopViewer:Visualise OMOP Results using 'shiny' Applications

Visualise results obtained from analysing data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model using 'shiny' applications.

Maintained by Martí Català. Last updated 19 days ago.

3 stars 6.15 score 4 scripts

patzaw

TKCat:Tailored Knowledge Catalog

Facilitate the management of data from knowledge resources that are frequently used alone or together in research environments. In 'TKCat', knowledge resources are manipulated as modeled database (MDB) objects. These objects provide access to the data tables along with a general description of the resource and a detail data model documenting the tables, their fields and their relationships. These MDBs are then gathered in catalogs that can be easily explored an shared. Finally, 'TKCat' provides tools to easily subset, filter and combine MDBs and create new catalogs suited for specific needs.

Maintained by Patrice Godard. Last updated 3 days ago.

5 stars 6.13 score 27 scripts

jsakaluk

dySEM:Dyadic Structural Equation Modeling

Scripting of structural equation models via 'lavaan' for Dyadic Data Analysis, and helper functions for supplemental calculations, tabling, and model visualization. Current models supported include Dyadic Confirmatory Factor Analysis, the Actor–Partner Interdependence Model (observed and latent), the Common Fate Model (observed and latent), Mutual Influence Model (latent), and the Bifactor Dyadic Model (latent).

Maintained by John Sakaluk. Last updated 3 days ago.

6 stars 6.12 score 10 scripts

bhaskarvk

colormap:Color Palettes using Colormaps Node Module

Allows to generate colors from palettes defined in the colormap module of 'Node.js'. (see <https://github.com/bpostlethwaite/colormap> for more information). In total it provides 44 distinct palettes made from sequential and/or diverging colors. In addition to the pre defined palettes you can also specify your own set of colors. There are also scale functions that can be used with 'ggplot2'.

Maintained by Bhaskar Karambelkar. Last updated 3 years ago.

color-palettes colormap ggplot2 ggplot2-scales palettes

58 stars 6.12 score 225 scripts

jmadinlab

habtools:Tools and Metrics for 3D Surfaces and Objects

A collection of functions for sampling and simulating 3D surfaces and objects and estimating metrics like rugosity, fractal dimension, convexity, sphericity, circularity, second moments of area and volume, and more.

Maintained by Nina Schiettekatte. Last updated 24 days ago.

12 stars 6.10 score 9 scripts

atorus-research

datasetjson:Read and Write CDISC Dataset JSON Files

Read, construct and write CDISC (Clinical Data Interchange Standards Consortium) Dataset JSON (JavaScript Object Notation) files, while validating per the Dataset JSON schema file, as described in CDISC (2023) <https://www.cdisc.org/standards/data-exchange/dataset-json>.

Maintained by Mike Stackhouse. Last updated 2 months ago.

cdisc dataset-json

16 stars 6.08 score 5 scripts

shanejorr

usincometaxes:Calculate Federal and State Income Taxes in the United States

Calculates federal and state income taxes in the United States. It acts as a wrapper to the NBER's TAXSIM 35 (<http://taxsim.nber.org/taxsim35/>) tax simulator. TAXSIM 35 conducts the calculations, while 'usincometaxes' prepares the data for TAXSIM 35, sends the data to TAXSIM 35's server or communicates with the Web Assembly file, retrieves the data, and places it into a data frame. All without the user worrying about this process.

Maintained by Shane Orr. Last updated 1 years ago.

13 stars 5.99 score 15 scripts

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 5 months ago.

baseball ggplot2 sportsdataverse

21 stars 5.97 score 111 scripts

frankkramer-lab

mully:Create, Modify and Visualize Multi-Layered Networks

Allows the user to create graphs with multiple layers. The user can also modify the layers, the nodes, and the edges. The graph can also be visualized. Zaynab Hammoud and Frank Kramer (2018) <doi:10.3390/genes9110519>. More about multilayered graphs and their usage can be found in our review paper: Zaynab Hammoud and Frank Kramer (2020) <doi:10.1186/s41044-020-00046-0>.

Maintained by Zaynab Hammoud. Last updated 2 years ago.

big-networks data-visualization graph-theory graphs igraph multilayer-networks node-colored-graphs

45 stars 5.95 score 6 scripts

agricolamz

lingglosses:Interlinear Glossed Linguistic Examples and Abbreviation Lists Generation

Helps to render interlinear glossed linguistic examples in html 'rmarkdown' documents and then semi-automatically compiles the list of glosses at the end of the document. It also provides a database of linguistic glosses.

Maintained by George Moroz. Last updated 24 days ago.

glosses glosses-list interlinear-gloss language-documentation linguistics rmarkdown typology

15 stars 5.88 score 167 scripts

bayer-group

adepro:A 'shiny' Application for the (Audio-)Visualization of Adverse Event Profiles

Contains a 'shiny' application called AdEPro (Animation of Adverse Event Profiles) which (audio-)visualizes adverse events occurring in clinical trials. As this data is usually considered sensitive, this tool is provided as a stand-alone application that can be launched from any local machine on which the data is stored.

Maintained by Nicole Rethemeier. Last updated 5 days ago.

adverse-events bayer-not-classified bayer-reg-none beat-not-applicable clinical-trials data-insights shiny-apps visualization

7 stars 5.84 score 11 scripts

agdamsbo

REDCapCAST:REDCap Metadata Casting and Castellated Data Handling

Casting metadata for REDCap database creation and handling of castellated data using repeated instruments and longitudinal projects in 'REDCap'. Keeps a focused data export approach, by allowing to only export required data from the database. Also for casting new REDCap databases based on datasets from other sources. Originally forked from the R part of 'REDCapRITS' by Paul Egeler. See <https://github.com/pegeler/REDCapRITS>. 'REDCap' (Research Electronic Data Capture) is a secure, web-based software platform designed to support data capture for research studies, providing 1) an intuitive interface for validated data capture; 2) audit trails for tracking data manipulation and export procedures; 3) automated export procedures for seamless data downloads to common statistical packages; and 4) procedures for data integration and interoperability with external sources (Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>; Harris et al (2019) <doi:10.1016/j.jbi.2019.103208>).

Maintained by Andreas Gammelgaard Damsbo. Last updated 19 days ago.

1 stars 5.84 score 12 scripts

mthulin

ivo.table:Nicely Formatted Contingency Tables and Frequency Tables

Nicely formatted frequency tables and contingency tables (1-way, 2-way, 3-way and 4-way tables), that can easily be exported to HTML or 'Office' documents. Designed to work with pipes.

Maintained by Måns Thulin. Last updated 1 months ago.

4 stars 5.81 score 6 scripts

mrc-ide

hintr:R API for calling naomi district level HIV model

R API for calling naomi district level HIV model.

Maintained by Robert Ashton. Last updated 18 days ago.

2 stars 5.80 score 2 scripts 1 dependents

adafede

cascade:Contextualizing untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts

This package provides the infrastructure to perform Automated Composition Assessment of Natural Extracts.

Maintained by Adriano Rutz. Last updated 1 days ago.

metabolite annotation charged aerosol detector semi-quantitative natural products computational metabolomics specialized metabolome

2 stars 5.76 score 40 scripts 1 dependents

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 scripts

kcf-jackson

sketch:Interactive Sketches

Creates static / animated / interactive visualisations embeddable in R Markdown documents. It implements an R-to-JavaScript transpiler and enables users to write JavaScript applications using the syntax of R.

Maintained by Chun Fung Kwok. Last updated 1 years ago.

javascript js transpiler visualisation

125 stars 5.70 score 27 scripts

frictionlessdata

tableschema.r:Table Schema 'Frictionless Data'

Allows to work with 'Table Schema' (<https://specs.frictionlessdata.io/table-schema/>). 'Table Schema' is well suited for use cases around handling and validating tabular data in text formats such as 'csv', but its utility extends well beyond this core usage, towards a range of applications where data benefits from a portable schema format. The 'tableschema.r' package can load and validate any table schema descriptor, allow the creation and modification of descriptors, expose methods for reading and streaming data that conforms to a 'Table Schema' via the 'Tabular Data Resource' abstraction.

Maintained by Kleanthis Koupidis. Last updated 2 years ago.

25 stars 5.70 score 101 scripts

inbo

camtrapdp:Read and Manipulate Camera Trap Data Packages

Read and manipulate Camera Trap Data Packages ('Camtrap DP'). 'Camtrap DP' (<https://camtrap-dp.tdwg.org>) is a data exchange format for camera trap data. With 'camtrapdp' you can read, filter and transform data (including to Darwin Core) before further analysis in e.g. 'camtraptor' or 'camtrapR'.

Maintained by Peter Desmet. Last updated 23 days ago.

camtrap-dp oscibio

7 stars 5.67 score 12 scripts

faasr

FaaSr:FaaS (Function as a Service) Package

Allows users to create and deploy the workflow with multiple functions in Function-as-a-Service (FaaS) cloud computing platforms. The 'FaaSr' package makes it simpler for R developers to use FaaS platforms by providing the following functionality: 1) Parsing and validating a JSON-based payload compliant to 'FaaSr' schema supporting multiple FaaS platforms 2) Invoking user functions written in R in a Docker container (derived from rocker), using a list generated from the parser as argument 3) Downloading/uploading of files from/to S3 buckets using simple primitives 4) Logging to files in S3 buckets 5) Triggering downstream actions supporting multiple FaaS platforms 6) Generating FaaS-specific API calls to simplify the registering of a user's workflow with a FaaS platform Supported FaaS platforms: Apache OpenWhisk <https://openwhisk.apache.org/> GitHub Actions <https://github.com/features/actions> Amazon Web Services (AWS) Lambda <https://aws.amazon.com/lambda/> Supported cloud data storage for persistent storage: Amazon Web Services (AWS) Simple Storage Service (S3) <https://aws.amazon.com/s3/>.

Maintained by Figueiredo Renato. Last updated 3 months ago.

7 stars 5.67 score 9 scripts

paithiov909

audubon:Japanese Text Processing Tools

A collection of Japanese text processing tools for filling Japanese iteration marks, Japanese character type conversions, segmentation by phrase, and text normalization which is based on rules for the 'Sudachi' morphological analyzer and the 'NEologd' (Neologism dictionary for 'MeCab'). These features are specific to Japanese and are not implemented in 'ICU' (International Components for Unicode).

Maintained by Akiru Kato. Last updated 11 days ago.

japanese javascript

10 stars 5.65 score 3 scripts 1 dependents

bioc

SEtools:SEtools: tools for working with SummarizedExperiment

This includes a set of convenience functions for working with the SummarizedExperiment class. Note that plotting functions historically in this package have been moved to the sechm package (see vignette for details).

Maintained by Pierre-Luc Germain. Last updated 5 months ago.

geneexpression

2 stars 5.64 score 72 scripts

mazamascience

MazamaLocationUtils:Manage Spatial Metadata for Known Locations

Utility functions for discovering and managing metadata associated with spatially unique "known locations". Applications include all fields of environmental monitoring (e.g. air and water quality) where data are collected at stationary sites.

Maintained by Jonathan Callahan. Last updated 4 months ago.

5.64 score 108 scripts

rafapereirabr

r5r:Rapid Realistic Routing with 'R5'

Rapid realistic routing on multimodal transport networks (walk, bike, public transport and car) using 'R5', the Rapid Realistic Routing on Real-world and Reimagined networks engine <https://github.com/conveyal/r5>. The package allows users to generate detailed routing analysis or calculate travel time and monetary cost matrices using seamless parallel computing on top of the R5 Java machine. While R5 is developed by Conveyal, the package r5r is independently developed by a team at the Institute for Applied Economic Research (Ipea) with contributions from collaborators. Apart from the documentation in this package, users will find additional information on R5 documentation at <https://docs.conveyal.com/>. Although we try to keep new releases of r5r in synchrony with R5, the development of R5 follows Conveyal's independent update process. Hence, users should confirm the R5 version implied by the Conveyal user manual (see <https://docs.conveyal.com/changelog>) corresponds with the R5 version that r5r depends on. This version of r5r depends on R5 v7.1.

Maintained by Rafael H. M. Pereira. Last updated 21 days ago.

openjdk

5.62 score 432 scripts

dnme-minturdep

comunicacion:DNMyE - Comunicación

Herramientas para la comunicación de la Dirección Nacional de Mercados y Estadística de la Subsecretaría de Turismo de Argentina.

Maintained by Juan Pablo Ruiz Nicolini. Last updated 8 months ago.

argentina estadistica openjdk

4 stars 5.57 score 124 scripts 1 dependents

luisdva

forgts:Convert Formatted Spreadsheets to Presentation-Ready Display Tables

Reads cell contents plus formatting from a spreadsheet file and creates an editable 'gt' object with the same data and formatting. Supports the most commonly-used cell and text styles including colors, fills, font weights and decorations, and borders.

Maintained by Luis D. Verde Arregoitia. Last updated 2 months ago.

18 stars 5.56 score 3 scripts

blakedickson

Morphoscape:Computation and Visualization of Adaptive Landscapes

Implements adaptive landscape methods first described by Polly et al. (2016) <doi:10.1080/02724634.2016.1111225> for the integration, analysis and visualization of biological trait data on a phenotypic morphospace - typically defined by shape metrics.

Maintained by Blake Dickson. Last updated 10 months ago.

4 stars 5.56 score 8 scripts

usaid-oha-si

mindthegap:Mind the Gap

Package to tidy UNAIDS estimates (from the EDMS database) as well as plot trends in UNAIDS 95 goals and ART coverage gap by country.

Maintained by Karishma Srikanth. Last updated 2 months ago.

5 stars 5.51 score 13 scripts

bioc

miRSM:Inferring miRNA sponge modules in heterogeneous data

The package aims to identify miRNA sponge or ceRNA modules in heterogeneous data. It provides several functions to study miRNA sponge modules at single-sample and multi-sample levels, including popular methods for inferring gene modules (candidate miRNA sponge or ceRNA modules), and two functions to identify miRNA sponge modules at single-sample and multi-sample levels, as well as several functions to conduct modular analysis of miRNA sponge modules.

Maintained by Junpeng Zhang. Last updated 5 months ago.

geneexpression biomedicalinformatics clustering genesetenrichment microarray software generegulation genetarget cerna mirna mirna-sponge mirna-targets modules openjdk

4 stars 5.51 score 5 scripts

r-barnes

webglobe:3D Interactive Globes

Displays geospatial data on an interactive 3D globe in the web browser.

Maintained by Richard Barnes. Last updated 5 years ago.

3d cesiumjs data-visualization globe visualization

30 stars 5.48 score 20 scripts

nflverse

nflverse:Easily Install and Load the 'nflverse'

The 'nflverse' is a set of packages dedicated to data of the National Football League. This package is designed to make it easy to install and load multiple 'nflverse' packages in a single step. Learn more about the 'nflverse' at <https://nflverse.nflverse.com/>.

Maintained by Sebastian Carl. Last updated 23 hours ago.

29 stars 5.47 score 204 scripts

bioc

alabaster.sce:Load and Save SingleCellExperiment from File

Save SingleCellExperiment into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Maintained by Aaron Lun. Last updated 5 months ago.

dataimport datarepresentation

5.43 score 4 scripts 3 dependents

luckinet

arealDB:Harmonise and Integrate Heterogeneous Areal Data

Many relevant applications in the environmental and socioeconomic sciences use areal data, such as biodiversity checklists, agricultural statistics, or socioeconomic surveys. For applications that surpass the spatial, temporal or thematic scope of any single data source, data must be integrated from several heterogeneous sources. Inconsistent concepts, definitions, or messy data tables make this a tedious and error-prone process. 'arealDB' tackles those problems and helps the user to integrate a harmonised databases of areal data. Read the paper at Ehrmann, Seppelt & Meyer (2020) <doi:10.1016/j.envsoft.2020.104799>.

Maintained by Steffen Ehrmann. Last updated 2 months ago.

areal-data database

2 stars 5.41 score 15 scripts

r-causal

halfmoon:Techniques to Build Better Balance

Build better balance in causal inference models. 'halfmoon' helps you assess propensity score models for balance between groups using metrics like standardized mean differences and visualization techniques like mirrored histograms. 'halfmoon' supports both weighting and matching techniques.

Maintained by Malcolm Barrett. Last updated 29 days ago.

17 stars 5.39 score 72 scripts

darwin-eu-dev

PaRe:A Way to Perform Code Review or QA on Other Packages

Reviews other packages during code review by looking at their dependencies, code style, code complexity, and how internally defined functions interact with one another.

Maintained by Maarten van Kessel. Last updated 4 months ago.

3 stars 5.38 score 20 scripts

gorkang

BayesianReasoning:Plot Positive and Negative Predictive Values for Medical Tests

Functions to plot and help understand positive and negative predictive values (PPV and NPV), and their relationship with sensitivity, specificity, and prevalence. See Akobeng, A.K. (2007) <doi:10.1111/j.1651-2227.2006.00180.x> for a theoretical overview of the technical concepts and Navarrete et al. (2015) for a practical explanation about the importance of their understanding <doi:10.3389/fpsyg.2015.01327>.

Maintained by Gorka Navarrete. Last updated 12 months ago.

bayesian-inference negative-predictive-value positive-predictive-value

8 stars 5.38 score 15 scripts

jhorzek

tablespan:Create Satisficing 'Excel', 'HTML', 'LaTeX', and 'RTF' Tables using a Simple Formula

Create "good enough" tables with a single formula. 'tablespan' tables can be exported to 'Excel', 'HTML', 'LaTeX', and 'RTF' by leveraging the packages 'openxlsx' and 'gt'. See <https://jhorzek.github.io/tablespan/> for an introduction.

Maintained by Jannik H. Orzek. Last updated 2 months ago.

excel html latex rtf tables

14 stars 5.36 score 30 scripts

bioc

MsQuality:MsQuality - Quality metric calculation from Spectra and MsExperiment objects

The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.

Maintained by Thomas Naake. Last updated 2 months ago.

metabolomics proteomics massspectrometry qualitycontrol mass-spectrometry qc

7 stars 5.32 score 2 scripts

elliecurnow

midoc:A Decision-Making System for Multiple Imputation

A guidance system for analysis with missing data. It incorporates expert, up-to-date methodology to help researchers choose the most appropriate analysis approach when some data are missing. You provide the available data and the assumed causal structure, including the likely causes of missing data. 'midoc' will advise which analysis approaches can be used, and how best to perform them. 'midoc' follows the framework for the treatment and reporting of missing data in observational studies (TARMOS). Lee et al (2021). <doi:10.1016/j.jclinepi.2021.01.008>.

Maintained by Elinor Curnow. Last updated 6 months ago.

missing-data multiple-imputation

6 stars 5.32 score 8 scripts

haghish

DOT:Render and Export DOT Graphs in R

Renders DOT diagram markup language in R and also provides the possibility to export the graphs in PostScript and SVG (Scalable Vector Graphics) formats. In addition, it supports literate programming packages such as 'knitr' and 'rmarkdown'.

Maintained by E. F. Haghish. Last updated 1 months ago.

2 stars 5.28 score 63 scripts 1 dependents

chawezimiti

BLA:Boundary Line Analysis

Fits boundary line models to datasets as proposed by Webb (1972) <doi:10.1080/00221589.1972.11514472> and makes statistical inferences about their parameters. Provides additional tools for testing datasets for evidence of boundary presence and selecting initial starting values for model optimization prior to fitting the boundary line models. It also includes tools for conducting post-hoc analyses such as predicting boundary values and identifying the most limiting factor (Miti, Milne, Giller, Lark (2024) <doi:10.1016/j.fcr.2024.109365>). This ensures a comprehensive analysis for datasets that exhibit upper boundary structures.

Maintained by Chawezi Miti. Last updated 4 months ago.

1 stars 5.26 score 11 scripts

harrison4192

validata:Validate Data Frames

Functions for validating the structure and properties of data frames. Answers essential questions about a data set after initial import or modification. What are the unique or missing values? What columns form a primary key? What are the properties of the numeric or categorical columns? What kind of overlap or mapping exists between 2 columns?

Maintained by Harrison Tietze. Last updated 24 days ago.

6 stars 5.26 score 4 scripts 1 dependents

forsterepi

epicmodel:Causal Modeling in Epidemiology

Create causal models for use in epidemiological studies, including sufficient-component cause models as introduced by Rothman (1976) <doi:10.1093/oxfordjournals.aje.a112335>.

Maintained by Felix Forster. Last updated 4 months ago.

5.24 score 6 scripts

chris31415926535

valhallr:A Tidy Interface to the 'Valhalla' Routing Engine

An interface to the 'Valhalla' routing engine’s application programming interfaces (APIs) for turn-by-turn routing, isochrones, and origin-destination analyses. Also includes several user-friendly functions for plotting outputs, and strives to follow "tidy" design principles. Please note that this package requires access to a running instance of 'Valhalla', which is open source and can be downloaded from <https://github.com/valhalla/valhalla>.

Maintained by Christopher Belanger. Last updated 3 years ago.

12 stars 5.21 score 27 scripts

bioc

gDR:Umbrella package for R packages in the gDR suite

Package is a part of the gDR suite. It reexports functions from other packages in the gDR suite that contain critical processing functions and utilities. The vignette walks through the full processing pipeline for drug response analyses that the gDR suite offers.

Maintained by Arkadiusz Gladki. Last updated 5 months ago.

software dataimport shinyapps

1 stars 5.20 score 7 scripts

rpuggaardrode

praatpicture:'Praat Picture' Style Plots of Acoustic Data

Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of flexibility. Also provides options for embedding audio in figures and animating figures.

Maintained by Rasmus Puggaard-Rode. Last updated 1 months ago.

31 stars 5.19 score 3 scripts

salbeke

rKIN:(Kernel) Isotope Niche Estimation

Applies methods used to estimate animal homerange, but instead of geospatial coordinates, we use isotopic coordinates. The estimation methods include: 1) 2-dimensional bivariate normal kernel utilization density estimator, 2) bivariate normal ellipse estimator, and 3) minimum convex polygon estimator, all applied to stable isotope data. Additionally, functions to determine niche area, polygon overlap between groups and levels (confidence contours) and plotting capabilities.

Maintained by Shannon E Albeke. Last updated 26 days ago.

4 stars 5.13 score 34 scripts

spsanderson

healthyverse:Easily Install and Load the 'healthyverse'

The 'healthyverse' 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 'healthyverse' packages in a single step.

Maintained by Steven Sanderson. Last updated 6 months ago.

analytics healthcare healthcare-application installation installer meta packages

11 stars 5.12 score 24 scripts

yuanchao-xu

gfer:Green Finance and Environmental Risk

Focuses on data collecting, analyzing and visualization in green finance and environmental risk research and analysis. Main function includes environmental data collecting from official websites such as MEP (Ministry of Environmental Protection of China, <https://www.mee.gov.cn>), water related projects identification and environmental data visualization.

Maintained by Yuanchao Xu. Last updated 10 days ago.

corporate-social-responsibility csr data-analysis data-scraping environmental-risk green-finance stock-data

8 stars 5.11 score 16 scripts

bioc

chevreulShiny:Tools for managing SingleCellExperiment objects as projects

Tools for managing SingleCellExperiment objects as projects. Includes functions for analysis and visualization of single-cell data. Also included is a shiny app for visualization of pre-processed scRNA data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Maintained by Kevin Stachelek. Last updated 26 days ago.

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

5.08 score

craig-parylo

plotor:Produces an Odds Ratio Plot from a Logistic Regression Model

Produces an Odds Ratio (OR) Plot to visualise the result of a logistic regression analysis. Provide it with a binomial regression model produced by 'glm()' and it will convert the estimates to odds ratios with a 95% confidence interval and plot the results using 'ggplot2'.

Maintained by Craig Parylo. Last updated 13 days ago.

ggplot2 glm logistic-regression odds-ratio

2 stars 5.04 score 7 scripts

bioc

alabaster.spatial:Save and Load Spatial 'Omics Data to/from File

Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Maintained by Aaron Lun. Last updated 5 months ago.

dataimport datarepresentation

5.02 score 5 scripts 1 dependents

dieghernan

pkgdev:Helpers to Develop a Package using GitHub Actions

A small set of functions that takes advantage of GitHub Actions for making your life easier as a R package developer. This package is primarily intended for personal use, however feel free to use it (at your own risk :)).

Maintained by Diego Hernangómez. Last updated 5 days ago.

developer-tools experimental github-actions

4 stars 5.00 score 7 scripts

bioc

broadSeq:broadSeq : for streamlined exploration of RNA-seq data

This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.

Maintained by Rishi Das Roy. Last updated 5 months ago.

geneexpression differentialexpression rnaseq transcriptomics sequencing coverage genesetenrichment go

4 stars 5.00 score 7 scripts

bioc

alabaster.string:Save and Load Biostrings to/from File

Save Biostrings objects to file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Maintained by Aaron Lun. Last updated 5 months ago.

dataimport datarepresentation

4.95 score 5 scripts 2 dependents

openwashdata

washr:Publication Toolkit for Water, Sanitation and Hygiene (WASH) Data

A toolkit to set up an R data package in a consistent structure. Automates tasks like tidy data export, data dictionary documentation, README and website creation, and citation management.

Maintained by Colin Walder. Last updated 5 months ago.

2 stars 4.95 score 7 scripts

stscl

geocn:Loads Spatial Data Sets of China

Providing various commonly used spatial data related to Chinese regions in the R programming environment.

Maintained by Wenbo Lv. Last updated 4 months ago.

china china-region geospatial-visualization maps

17 stars 4.93 score 10 scripts

bluegreen-labs

appeears:Interface to 'AppEEARS' NASA Web Services

Programmatic interface to the NASA Application for Extracting and Exploring Analysis Ready Samples services (AppEEARS; <https://appeears.earthdatacloud.nasa.gov/>). The package provides easy access to analysis ready earth observation data in R.

Maintained by Koen Hufkens. Last updated 1 months ago.

api data-science remote-sensing

11 stars 4.92 score 15 scripts

nmfs-ost

satf:Stock Assessment Tables and Figures

Creates exploratory and finished tables and figures for stock assessment documents from U.S. stock assessment model outputs. This packages addresses parts of the stock assessment workflow that interprets outputs of stock assessment models as well as allows the analyst to create report ready tables and figures, reducing the need to create their own and format then when adding into a report. This package is intended to be used in conjuction with `asar`, a partially automated template for writing various stock assessment reports. Throughout development, we will be creating a set of standardized figures and tables for a stock assessment report, developing functions to produce a variety of diagonostic plots, and other helpful materials. The advantage of using this package over others is that it applies to a range of stock assessment model outputs and standardizes them.

Maintained by Samantha Schiano. Last updated 1 months ago.

2 stars 4.88 score 5 scripts

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

zzawadz

dragulaR:Drag and Drop Elements in 'Shiny' using 'Dragula Javascript Library'

Move elements between containers in 'Shiny' without explicitly using 'JavaScript'. It can be used to build custom inputs or to change the positions of user interface elements like plots or tables.

Maintained by Zygmunt Zawadzki. Last updated 5 years ago.

drag-and-drop shiny

62 stars 4.83 score 22 scripts

korap

RKorAPClient:'KorAP' Web Service Client Package

A client package that makes the 'KorAP' web service API accessible from R. The corpus analysis platform 'KorAP' has been developed as a scientific tool to make potentially large, stratified and multiply annotated corpora, such as the 'German Reference Corpus DeReKo' or the 'Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify hypotheses and to find interesting patterns in real language use. The 'RKorAPClient' package provides access to 'KorAP' and the corpora behind it for user-created R code, as a programmatic alternative to the 'KorAP' web user-interface. You can learn more about 'KorAP' and use it directly on 'DeReKo' at <https://korap.ids-mannheim.de/>.

Maintained by Marc Kupietz. Last updated 28 days ago.

6 stars 4.81 score 30 scripts

mappinguniverse

mapping:Automatic Download, Linking, Manipulating Coordinates for Maps

Maps are an important tool to visualise variables distribution across different spatial objects. The mapping process requires to link the data with coordinates and then generate the correspondent map. This package provide coordinates, linking and mapping functions for an automatic, flexible and easy approach of external functions. The package provides an easy, flexible and automatic unit. Geographical coordinates are provided in the package and automatically linked with the input data to generate maps with internal provided functions or external functions. Provide an easy, flexible and automatic approach to potentially download updated coordinates, to link statistical units with coordinates and to aggregate variables based on the spatial hierarchy of units. The object returned from the package can be used for thematic maps with the build-in functions provided in mapping or with other packages already available.

Maintained by Alessio Serafini. Last updated 1 years ago.

4 stars 4.79 score 31 scripts

genentech

BayesERtools:Bayesian Exposure-Response Analysis Tools

Suite of tools that facilitate exposure-response analysis using Bayesian methods. The package provides a streamlined workflow for fitting types of models that are commonly used in exposure-response analysis - linear and Emax for continuous endpoints, logistic linear and logistic Emax for binary endpoints, as well as performing simulation and visualization. Learn more about the workflow at <https://genentech.github.io/BayesERbook/>.

Maintained by Kenta Yoshida. Last updated 1 months ago.

2 stars 4.78 score 20 scripts

bioc

alabaster.mae:Load and Save MultiAssayExperiments

Save MultiAssayExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Maintained by Aaron Lun. Last updated 5 months ago.

dataimport datarepresentation

4.78 score 5 scripts 1 dependents

harrison4192

tidybins:Make Tidy Bins

Multiple ways to bin numeric columns with a tidy output. Wraps a variety of existing binning methods into one function, and includes a new method for binning by equal value, which is useful for sales data. Provides a function to automatically summarize the properties of the binned columns.

Maintained by Harrison Tietze. Last updated 10 months ago.

4 stars 4.78 score 2 scripts 1 dependents

ddediu

AdhereRViz:Adherence to Medications

Interactive graphical user interface (GUI) for the package 'AdhereR', allowing the user to access different data sources, to explore the patterns of medication use therein, and the computation of various measures of adherence. It is implemented using Shiny and HTML/CSS/JavaScript.

Maintained by Dan Dediu. Last updated 1 years ago.

adherence-to-medications electronic-healthcare-data hadoop medical-databases medication-histories python sql visualisation

28 stars 4.75 score 2 scripts

sumanm47

BSTZINB:Association Among Disease Counts and Socio-Environmental Factors

Estimation of association between disease or death counts (e.g. COVID-19) and socio-environmental risk factors using a zero-inflated Bayesian spatiotemporal model. Non-spatiotemporal models and/or models without zero-inflation are also included for comparison. Functions to produce corresponding maps are also included. See Chakraborty et al. (2022) <doi:10.1007/s13253-022-00487-1> for more details on the method.

Maintained by Suman Majumder. Last updated 2 months ago.

4.70 score 2 scripts

trackerproject

trackeRapp:Interface for the Analysis of Running, Cycling and Swimming Data from GPS-Enabled Tracking Devices

Provides an integrated user interface and workflow for the analysis of running, cycling and swimming data from GPS-enabled tracking devices through the 'trackeR' <https://CRAN.R-project.org/package=trackeR> R package.

Maintained by Ioannis Kosmidis. Last updated 3 years ago.

data-visualization shiny sports-app web-app web-development

32 stars 4.68 score 2 scripts

elipousson

getACS:Help Wrangling American Community Survey Data from tidycensus

A package with helper functions for working with Census data downloaded with the tidycensus package.

Maintained by Eli Pousson. Last updated 2 months ago.

american-community-survey tidycensus

4 stars 4.68 score 10 scripts

hubverse-org

hubValidations:Testing framework for hubverse hub validations

This package aims at providing a simple interface to run validations on data and metadata submitted to a hubverse modeling hub. Validation tests can be run at different levels (single file, single folder, whole repository) and locally as well as part of a continuous integration workflow.

Maintained by Anna Krystalli. Last updated 17 days ago.

hubverse

1 stars 4.67 score 27 scripts 1 dependents

inbo

movepub:Prepare Movebank Data for Publication

Prepare animal tracking data from 'Movebank' (<https://movebank.org>) for publication in a research repository. With 'movepub' you can document data with metadata following the Data Package standard and transform these to Darwin Core and Ecological Metadata Language ('EML') for publication to the Global Biodiversity Information Facility ('GBIF') and the Ocean Biodiversity Information System ('OBIS').

Maintained by Peter Desmet. Last updated 16 days ago.

oscibio

3 stars 4.65 score 5 scripts

bioc

alabaster.bumpy:Save and Load BumpyMatrices to/from file

Save BumpyMatrix objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Maintained by Aaron Lun. Last updated 5 months ago.

dataimport datarepresentation

4.65 score 5 scripts 1 dependents

bioc

alabaster.vcf:Save and Load Variant Data to/from File

Save variant calling SummarizedExperiment to file and load them back as VCF objects. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Maintained by Aaron Lun. Last updated 5 months ago.

dataimport datarepresentation

4.65 score 6 scripts 1 dependents

bioc

Summix:Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data

This package contains the Summix2 method for estimating and adjusting for substructure in genetic summary allele frequency data. The function summix() estimates reference group proportions using a mixture model. The adjAF() function produces adjusted allele frequencies for an observed group with reference group proportions matching a target individual or sample. The summix_local() function estimates local ancestry mixture proportions and performs selection scans in genetic summary data.

Maintained by Audrey Hendricks. Last updated 5 months ago.

statisticalmethod wholegenome genetics

4.62 score 14 scripts

bioc

CARDspa:Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

CARD is a reference-based deconvolution method that estimates cell type composition in spatial transcriptomics based on cell type specific expression information obtained from a reference scRNA-seq data. A key feature of CARD is its ability to accommodate spatial correlation in the cell type composition across tissue locations, enabling accurate and spatially informed cell type deconvolution as well as refined spatial map construction. CARD relies on an efficient optimization algorithm for constrained maximum likelihood estimation and is scalable to spatial transcriptomics with tens of thousands of spatial locations and tens of thousands of genes.

Maintained by Jing Fu. Last updated 2 days ago.

spatial singlecell transcriptomics visualization openblas cpp openmp

4.60 score 3 scripts

shixiangwang

tinyscholar:Get and Show Personal 'Google Scholar' Profile

Provides functions to get personal 'Google Scholar' profile data from web API and show it in table or figure format.

Maintained by Shixiang Wang. Last updated 1 years ago.

google-scholar

8 stars 4.60 score 7 scripts

ggseg

ggsegExtra:Extra Utilities for the 'ggseg' and 'ggseg3d' Plotting Tools

Contains functions to create new data sets compatible with the 'ggseg' and 'ggseg3d' packages for plotting brain segmentations through R. Requires several external software to be installed on the system for atlas creations to work, and most of these are not available for windows. But atlas creation tools exist for 2d simple features data, and also 3d tri-surface mesh plots. Also has a list of compatible data sets and functions for easy installation of these.

Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.

55 stars 4.59 score 70 scripts

ropensci

prismjs:Server-Side Syntax Highlighting

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

Maintained by Jeroen Ooms. Last updated 3 months ago.

5 stars 4.57 score 1 scripts 1 dependents

rich-iannone

omsvg:Build and Transform 'SVG' Objects

Build 'SVG' components using element-based functions. With an 'svg' object, we can modify its graphical elements with a suite of transform functions.

Maintained by Richard Iannone. Last updated 4 years ago.

easy-to-use svg

51 stars 4.55 score 14 scripts

sergejruff

Virusparies:Visualize and Process Output from 'VirusHunterGatherer'

A collection of tools for downstream analysis of 'VirusHunterGatherer' output. Processing of hittables and plotting of results, enabling better interpretation, is made easier with the provided functions.

Maintained by Ruff Sergej. Last updated 4 months ago.

bioinformatics data-driven discover discovery ggplot2 graphical-table hidden-markov-model hmmlearn plot r-programming summary-statistics virus virus-discovery virus-scanning virusgatherer virushunter virushuntergatherer visualization

1 stars 4.49 score 28 scripts

r4epi

sitrep:Report templates and helper functions for applied epidemiology

Report templates and helper functions for applied epidemiology.

Maintained by Alexander Spina. Last updated 23 days ago.

epidemiology msf outbreaks report-generator

41 stars 4.46 score 9 scripts

katynasada

ODT:Optimal Decision Trees Algorithm

Implements a tree-based method specifically designed for personalized medicine applications. By using genomic and mutational data, 'ODT' efficiently identifies optimal drug recommendations tailored to individual patient profiles. The 'ODT' algorithm constructs decision trees that bifurcate at each node, selecting the most relevant markers (discrete or continuous) and corresponding treatments, thus ensuring that recommendations are both personalized and statistically robust. This iterative approach enhances therapeutic decision-making by refining treatment suggestions until a predefined group size is achieved. Moreover, the simplicity and interpretability of the resulting trees make the method accessible to healthcare professionals. Includes functions for training the decision tree, making predictions on new samples or patients, and visualizing the resulting tree. For detailed insights into the methodology, please refer to Gimeno et al. (2023) <doi:10.1093/bib/bbad200>.

Maintained by Katyna Sada Del Real. Last updated 4 days ago.

4.40 score 1 scripts

bioc

alabaster.files:Wrappers to Save Common File Formats

Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.

Maintained by Aaron Lun. Last updated 5 months ago.

datarepresentation dataimport

4.32 score 21 scripts

petermeissner

ical:'iCalendar' Parsing

A simple wrapper around the 'ical.js' library executing 'Javascript' code via 'V8' (the 'Javascript' engine driving the 'Chrome' browser and 'Node.js' and accessible via the 'V8' R package). This package enables users to parse 'iCalendar' files ('.ics', '.ifb', '.iCal', '.iFBf') into lists and 'data.frames' to ultimately do statistics on events, meetings, schedules, birthdays, and the like.

Maintained by Peter Meissner. Last updated 5 years ago.

ical icalendar-parsing v8

18 stars 4.32 score 23 scripts

bioc

BloodGen3Module:This R package for performing module repertoire analyses and generating fingerprint representations

The BloodGen3Module package provides functions for R user performing module repertoire analyses and generating fingerprint representations. Functions can perform group comparison or individual sample analysis and visualization by fingerprint grid plot or fingerprint heatmap. Module repertoire analyses typically involve determining the percentage of the constitutive genes for each module that are significantly increased or decreased. As we describe in details;https://www.biorxiv.org/content/10.1101/525709v2 and https://pubmed.ncbi.nlm.nih.gov/33624743/, the results of module repertoire analyses can be represented in a fingerprint format, where red and blue spots indicate increases or decreases in module activity. These spots are subsequently represented either on a grid, with each position being assigned to a given module, or in a heatmap where the samples are arranged in columns and the modules in rows.

Maintained by Darawan Rinchai. Last updated 5 months ago.

software visualization geneexpression

4.30 score 5 scripts

ffverse

ffpros:Retrieves Data from FantasyPros

Helps gather data from FantasyPros.com with rate-limiting/caching, forming appropriate calls, and returning tidy dataframes which can be easily connected to other data sources.

Maintained by Tan Ho. Last updated 10 months ago.

fantasy-football fantasypros

9 stars 4.30 score 22 scripts

tysonstanley

MarginalMediation:Marginal Mediation

Provides the ability to perform "Marginal Mediation"--mediation wherein the indirect and direct effects are in terms of the average marginal effects (Bartus, 2005, <https://EconPapers.repec.org/RePEc:tsj:stataj:v:5:y:2005:i:3:p:309-329>). The style of the average marginal effects stems from Thomas Leeper's work on the "margins" package. This framework allows the use of categorical mediators and outcomes with little change in interpretation from the continuous mediators/outcomes. See <doi:10.13140/RG.2.2.18465.92001> for more details on the method.

Maintained by Tyson S Barrett. Last updated 3 years ago.

average-marginal-effects margins mediation mediation-analysis mediator partial-effects rstudio

3 stars 4.29 score 13 scripts

estadisticaun

UnalR:Una implementación de funciones de uso interno

Una herramienta rápida y consistente para la disposición de microdatos y la visualización de las cifras y estadísticas oficiales de la Universidad Nacional de Colombia <https://unal.edu.co>. Contiene una biblioteca de funciones gráficas, tanto estáticas como interactivas, que ofrece numerosos tipos de gráficos con una sintaxis altamente configurable y simple. Entre estos encontramos la visualización de tablas HTML, series, gráficos de barras y circulares, mapas, etc. Todo lo anterior apoyado en bibliotecas de JavaScript. English: A fast and consistent tool for the arrangement of microdata and the visualization of official figures and statistics from the National University of Colombia <https://unal.edu.co>. It includes a library of graphical functions, both static and interactive, offering numerous types of charts with a highly configurable and simple syntax. Among these, we find the visualization of HTML tables, series, bar and pie charts, maps, etc. It provides the capability to transition from the interactive to the dynamic world and from one library to another without changing function or syntax.

Maintained by Jeison Alarcón. Last updated 7 months ago.

2 stars 4.28 score 21 scripts

lance-waller-lab

envi:Environmental Interpolation using Spatial Kernel Density Estimation

Estimates an ecological niche using occurrence data, covariates, and kernel density-based estimation methods. For a single species with presence and absence data, the 'envi' package uses the spatial relative risk function that is estimated using the 'sparr' package. Details about the 'sparr' package methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.

Maintained by Ian D. Buller. Last updated 5 months ago.

ecological-niche ecological-niche-modelling geospatial geospatial-analysis kernel-density-estimation niche-modeling niche-modelling non-euclidean-spaces point-pattern point-pattern-analysis principal-component-analysis spatial-analysis species-distribution-modeling species-distribution-modelling

1 stars 4.22 score 33 scripts

ropensci

postdoc:Minimal and Uncluttered Package Documentation

Generates simple and beautiful one-page HTML reference manuals with package documentation. Math rendering and syntax highlighting are done server-side in R such that no JavaScript libraries are needed in the browser, which makes the documentation portable and fast to load.

Maintained by Jeroen Ooms. Last updated 6 months ago.

11 stars 4.22 score 2 scripts

peleplay

integr:An Implementation of Interaction Graphs of Aleks Jakulin

Generates a 'Graphviz' graph of the most significant 3-way interaction gains (i.e. conditional information gains) based on a provided discrete data frame. Various output formats are supported ('Graphviz', SVG, PNG, PDF, PS). For references, see the webpage of Aleks Jakulin <http://stat.columbia.edu/~jakulin/Int/>.

Maintained by Petar Markovic. Last updated 6 years ago.

3 stars 4.18 score 3 scripts

agdamsbo

stRoke:Clinical Stroke Research

A collection of tools for clinical trial data management and analysis in research and teaching. The package is mainly collected for personal use, but any use beyond that is encouraged. This package has migrated functions from 'agdamsbo/daDoctoR', and new functions has been added. Version follows months and year. See NEWS/Changelog for release notes. This package includes sampled data from the TALOS trial (Kraglund et al (2018) <doi:10.1161/STROKEAHA.117.020067>). The win_prob() function is based on work by Zou et al (2022) <doi:10.1161/STROKEAHA.121.037744>. The age_calc() function is based on work by Becker (2020) <doi:10.18637/jss.v093.i02>.

Maintained by Andreas Gammelgaard Damsbo. Last updated 5 months ago.

neuroscience stroke

4.18 score 7 scripts

gsk-biostatistics

tfrmtbuilder:'shiny' App Companion to the 'tfrmt' Package

Provides an interactive interface to the 'tfrmt' package. Users can import, modify, and export tables and templates with little to no code.

Maintained by Becca Krouse. Last updated 7 months ago.

5 stars 4.18 score 9 scripts

christopherkenny

dots:Dot Density Maps

Generate point data for representing people within spatial data. This collects a suite of tools for creating simple dot density maps. Several functions from different spatial packages are standardized to take the same arguments so that they can be easily substituted for each other.

Maintained by Christopher T. Kenny. Last updated 2 years ago.

3 stars 4.18 score 8 scripts

olehprylutskyi

spectralR:Obtain and Visualize Spectral Reflectance Data for Earth Surface Polygons

Tools for obtaining, processing, and visualizing spectral reflectance data for the user-defined land or water surface classes for visual exploring in which wavelength the classes differ. Input should be a shapefile with polygons of surface classes (it might be different habitat types, crops, vegetation, etc.). The Sentinel-2 L2A satellite mission optical bands pixel data are obtained through the Google Earth Engine service (<https://earthengine.google.com/>) and used as a source of spectral data.

Maintained by Oleh Prylutskyi. Last updated 2 years ago.

10 stars 4.18 score 1 scripts

dhaine

apisensr:Interface to 'episensr' for Sensitivity Analysis of Epidemiological Results

API for using 'episensr', Basic sensitivity analysis of the observed relative risks adjusting for unmeasured confounding and misclassification of the exposure/outcome, or both. See <https://cran.r-project.org/package=episensr>.

Maintained by Denis Haine. Last updated 2 years ago.

3 stars 4.18 score 5 scripts

barbaratarantino

SEMdeep:Structural Equation Modeling with Deep Neural Network and Machine Learning

Training and validation of a custom (or data-driven) Structural Equation Models using layer-wise Deep Neural Networks or node-wise Machine Learning algorithms, which extend the fitting procedures of the 'SEMgraph' R package <doi:10.32614/CRAN.package.SEMgraph>.

Maintained by Barbara Tarantino. Last updated 2 months ago.

4 stars 4.15 score

epicentre-msf

epivis:Tools for visualising epidemiological data

Static visualisation of patient level linelist data.

Maintained by Paul Campbell. Last updated 5 months ago.

3 stars 4.13 score 3 scripts

rformassspectrometry

MsIO:Serializing and restoring/importing mass spectrometry data objects

The serialization mechanism of R allows to save and load R data objects in a binary format, that can however not be read by other programming languages or software. The MsIO package supports serializing and restoring or importing mass spectrometry data objects to and from language agnostic file formats. A variety of different file types, including HDF5 and JSON-based formats defined by the Bioconductor *alabaster* package are supported. The file type can be defined and configured through a second argument `param` of the export/import methods.

Maintained by Johannes Rainer. Last updated 11 days ago.

infrastructure massspectrometry metabolomics dataimport proteomics mass-spectrometry

2 stars 4.11 score 5 scripts

eduardoarle

bRacatus:A Method to Estimate the Accuracy and Biogeographical Status of Georeferenced Biological Data

Automated assessment of accuracy and geographical status of georeferenced biological data. The methods rely on reference regions, namely checklists and range maps. Includes functions to obtain data from the Global Biodiversity Information Facility <https://www.gbif.org/> and from the Global Inventory of Floras and Traits <https://gift.uni-goettingen.de/home>. Alternatively, the user can input their own data. Furthermore, provides easy visualisation of the data and the results through the plotting functions. Especially suited for large datasets. The reference for the methodology is: Arlé et al. (under review).

Maintained by Eduardo Arlé. Last updated 11 months ago.

8 stars 4.08 score 4 scripts

sbg

biocompute:Create and Manipulate BioCompute Objects

Tools to create, validate, and export BioCompute Objects described in King et al. (2019) <doi:10.17605/osf.io/h59uh>. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard. A checksum validator and a JSON schema validator are provided. This package also supports exporting BioCompute Objects as JSON, PDF, HTML, or 'Word' documents, and exporting to cloud-based platforms.

Maintained by Soner Koc. Last updated 10 months ago.

biocompute biocompute-objects bioinformatics science-communication sevenbridges standardization workflow

3 stars 4.07 score 13 scripts

oxfordihtm

pactr:An Interface to the Pandemic PACT Database

The Pandemic PACT <https://www.pandemicpact.org/> monitors and analyses global funding and research evidence related to diseases with pandemic potential, as well as broader research preparedness efforts, and is equipped to pivot in response to outbreaks. It collects, curates, codes, and analyses data in alignment with WHO priority diseases and other selected illnesses, including pandemic influenza, mpox, and plague. Pandemic PACT aims to guide policy and decision-making for research funders, policymakers, researchers, multilateral agencies. The database is publicly available for download from its website and from Figshare. This package interfaces with the project's Figshare repository to provide programmatic access to the database along with other data products provided by the project.

Maintained by Ernest Guevarra. Last updated 5 months ago.

1 stars 4.07 score 13 scripts

cysouw

qlcVisualize:Visualization for Quantitative Language Comparison

Collection of visualizations as used in quantitative language comparison. Currently implemented are visualisations dealing nominal data with multiple levels ("level map" and "factor map"), and assistance for making weighted geographical Voronoi-maps ("weighted map").

Maintained by Michael Cysouw. Last updated 6 months ago.

4.03 score 24 scripts

kiangkiangkiang

ggESDA:Exploratory Symbolic Data Analysis with 'ggplot2'

Implements an extension of 'ggplot2' and visualizes the symbolic data with multiple plot which can be adjusted by more general and flexible input arguments. It also provides a function to transform the classical data to symbolic data by both clustering algorithm and customized method.

Maintained by Bo-Syue Jiang. Last updated 2 years ago.

21 stars 4.02 score 9 scripts

bioc

scTensor:Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition

The algorithm is based on the non-negative tucker decomposition (NTD2) of nnTensor.

Maintained by Koki Tsuyuzaki. Last updated 5 months ago.

dimensionreduction singlecell software geneexpression

4.00 score 2 scripts

politicaargentina

opinAr:Argentina's Public Opinion Toolbox

A toolbox for working with public opinion data from Argentina. It facilitates access to microdata and the calculation of indicators of the Trust in Government Index (ICG), prepared by the Torcuato Di Tella University. Although we will try to document everything possible in English, by its very nature Spanish will be the main language. El paquete fue pensado como una caja de herramientas para el trabajo con datos de opinión pública de Argentina. El mismo facilita el acceso a los microdatos y el cálculos de indicadores del Índice de Confianza en el Gobierno (ICG), elaborado por la Universidad Torcuato Di Tella.

Maintained by Juan Pablo Ruiz Nicolini. Last updated 1 years ago.

argentina data political-science politics public-opinion

4.00 score

ciirc-kso

rless:Leaner Style Sheets

Converts LESS to CSS. It uses V8 engine, where LESS parser is run. Functions for LESS text, file or folder conversion are provided. This work was supported by a junior grant research project by Czech Science Foundation 'GACR' no. 'GJ18-04150Y'.

Maintained by Jonas Vaclavek. Last updated 6 years ago.

css less shiny

1 stars 4.00 score 8 scripts

hubverse-org

hubverse:Easily Install and Load the 'hubverse'

A collection of packages that enables collaborative modeling exercises through a unified framework for aggregating, visualizing, and evaluating forecasts. This package is designed to make it easy to install and load multiple 'hubverse' packages in a single step. Learn more at <https://hubverse.io/en/latest/index.html>.

Maintained by Li Shandross. Last updated 6 months ago.

4.00 score 5 scripts