Showing 200 of total 2551 results (show query)
tiledb-inc
tiledb:Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays
The modern database 'TileDB' introduces a powerful on-disk format for storing and accessing any complex data based on multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations. This package provides the R support.
Maintained by Isaiah Norton. Last updated 5 days ago.
arrayhdfss3storage-managertiledbcpp
96.8 match 107 stars 11.96 score 306 scripts 4 dependentsjosesamos
starschemar:Obtaining Stars from Flat Tables
Data in multidimensional systems is obtained from operational systems and is transformed to adapt it to the new structure. Frequently, the operations to be performed aim to transform a flat table into a star schema. Transformations can be carried out using professional extract, transform and load tools or tools intended for data transformation for end users. With the tools mentioned, this transformation can be carried out, but it requires a lot of work. The main objective of this package is to define transformations that allow obtaining stars from flat tables easily. In addition, it includes basic data cleaning, dimension enrichment, incremental data refresh and query operations, adapted to this context.
Maintained by Jose Samos. Last updated 11 months ago.
108.8 match 7 stars 5.66 score 11 scripts 2 dependentsr-lib
ps:List, Query, Manipulate System Processes
List, query and manipulate all system processes, on 'Windows', 'Linux' and 'macOS'.
Maintained by Gรกbor Csรกrdi. Last updated 17 days ago.
33.4 match 79 stars 15.09 score 108 scripts 1.5k dependentsr-dbi
DBI:R Database Interface
A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.
Maintained by Kirill Mรผller. Last updated 3 months ago.
23.5 match 302 stars 20.88 score 19k scripts 2.9k dependentspecanproject
PEcAn.DB:PEcAn Functions Used for Ecological Forecasts and Reanalysis
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.
Maintained by David LeBauer. Last updated 3 days ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants
35.6 match 216 stars 11.88 score 127 scripts 27 dependentshenrikbengtsson
R.utils:Various Programming Utilities
Utility functions useful when programming and developing R packages.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
29.4 match 63 stars 13.74 score 5.7k scripts 814 dependentsropensci
osmdata:Import 'OpenStreetMap' Data as Simple Features or Spatial Objects
Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server (<https://overpass-api.de/>) and processed with very fast 'C++' routines for return to 'R'.
Maintained by Mark Padgham. Last updated 1 months ago.
open0street0mapopenstreetmapoverpass0apiosmcpposm-dataoverpass-apipeer-reviewedcpp
27.6 match 322 stars 14.53 score 2.8k scripts 14 dependentspharmaverse
admiral:ADaM in R Asset Library
A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>).
Maintained by Ben Straub. Last updated 5 days ago.
cdiscclinical-trialsopen-source
28.4 match 236 stars 13.89 score 486 scripts 4 dependentsr-lib
pak:Another Approach to Package Installation
The goal of 'pak' is to make package installation faster and more reliable. In particular, it performs all HTTP operations in parallel, so metadata resolution and package downloads are fast. Metadata and package files are cached on the local disk as well. 'pak' has a dependency solver, so it finds version conflicts before performing the installation. This version of 'pak' supports CRAN, 'Bioconductor' and 'GitHub' packages as well.
Maintained by Gรกbor Csรกrdi. Last updated 2 days ago.
27.7 match 717 stars 13.05 score 277 scripts 17 dependentsstevenmmortimer
salesforcer:An Implementation of 'Salesforce' APIs Using Tidy Principles
Functions connecting to the 'Salesforce' Platform APIs (REST, SOAP, Bulk 1.0, Bulk 2.0, Metadata, Reports and Dashboards) <https://trailhead.salesforce.com/content/learn/modules/api_basics/api_basics_overview>. "API" is an acronym for "application programming interface". Most all calls from these APIs are supported as they use CSV, XML or JSON data that can be parsed into R data structures. For more details please see the 'Salesforce' API documentation and this package's website <https://stevenmmortimer.github.io/salesforcer/> for more information, documentation, and examples.
Maintained by Steven M. Mortimer. Last updated 4 months ago.
api-wrappersr-languager-programmingsalesforcesalesforce-apis
38.1 match 82 stars 9.27 score 191 scriptscran
epiR:Tools for the Analysis of Epidemiological Data
Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Maintained by Mark Stevenson. Last updated 2 months ago.
42.4 match 10 stars 8.18 score 10 dependentsropensci
redland:RDF Library Bindings in R
Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <https://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.
Maintained by Matthew B. Jones. Last updated 1 years ago.
43.9 match 17 stars 7.85 score 98 scripts 13 dependentsmjg211
phaseR:Phase Plane Analysis of One- And Two-Dimensional Autonomous ODE Systems
Performs a qualitative analysis of one- and two-dimensional autonomous ordinary differential equation systems, using phase plane methods. Programs are available to identify and classify equilibrium points, plot the direction field, and plot trajectories for multiple initial conditions. In the one-dimensional case, a program is also available to plot the phase portrait. Whilst in the two-dimensional case, programs are additionally available to plot nullclines and stable/unstable manifolds of saddle points. Many example systems are provided for the user. For further details can be found in Grayling (2014) <doi:10.32614/RJ-2014-023>.
Maintained by Michael J Grayling. Last updated 3 years ago.
biological-modelingdifferential-equationsdynamical-systemsecological-modellinglotka-volterramanifoldsmodeling-dynamic-systemsmorris-lecarperturbation-analysisphase-planesir-modelspecies-interactionsvan-der-pol
51.2 match 15 stars 6.63 score 94 scripts 1 dependentsmllg
batchtools:Tools for Computation on Batch Systems
As a successor of the packages 'BatchJobs' and 'BatchExperiments', this package provides a parallel implementation of the Map function for high performance computing systems managed by schedulers 'IBM Spectrum LSF' (<https://www.ibm.com/products/hpc-workload-management>), 'OpenLava' (<https://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid Engine' (<https://www.univa.com/>), 'Slurm' (<https://slurm.schedmd.com/>), 'TORQUE/PBS' (<https://adaptivecomputing.com/cherry-services/torque-resource-manager/>), or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>). A multicore and socket mode allow the parallelization on a local machines, and multiple machines can be hooked up via SSH to create a makeshift cluster. Moreover, the package provides an abstraction mechanism to define large-scale computer experiments in a well-organized and reproducible way.
Maintained by Michel Lang. Last updated 2 years ago.
batchexperimentsbatchjobsdocker-swarmhigh-performance-computinghpchpc-clusterslsfopenlavaparallel-computingreproducibilitysgeslurmtorque
29.6 match 175 stars 11.39 score 772 scripts 14 dependentsohdsi
DatabaseConnector:Connecting to Various Database Platforms
An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server', 'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', 'Snowflake', 'Spark', 'SQLite', and 'InterSystems IRIS'). Also includes support for fetching data as 'Andromeda' objects. Uses either 'Java Database Connectivity' ('JDBC') or other 'DBI' drivers to connect to databases.
Maintained by Martijn Schuemie. Last updated 2 months ago.
26.3 match 56 stars 12.63 score 772 scripts 11 dependentsmiraisolutions
XLConnect:Excel Connector for R
Provides comprehensive functionality to read, write and format Excel data.
Maintained by Martin Studer. Last updated 19 days ago.
cross-platformexcelr-languagexlconnectopenjdk
25.2 match 130 stars 12.28 score 1.2k scripts 1 dependentsrpolars
polars:Lightning-Fast 'DataFrame' Library
Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.
Maintained by Soren Welling. Last updated 4 days ago.
25.8 match 499 stars 12.01 score 1.0k scripts 2 dependentsdataoneorg
dataone:R Interface to the DataONE REST API
Provides read and write access to data and metadata from the DataONE network <https://www.dataone.org> of data repositories. Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository. Users can also insert and update data objects on repositories that support these methods.
Maintained by Matthew B. Jones. Last updated 3 years ago.
29.6 match 36 stars 9.93 score 472 scripts 3 dependentshms-dbmi
UpSetR:A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
Creates visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks (Conway 2017) <doi:10.1093/bioinformatics/btx364>.
Maintained by Jake Conway. Last updated 4 years ago.
gehlenborglabggplot2upsetupsetrvisualization
18.8 match 781 stars 15.33 score 4.8k scripts 42 dependentsjosesamos
rolap:Obtaining Star Databases from Flat Tables
Data in multidimensional systems is obtained from operational systems and is transformed to adapt it to the new structure. Frequently, the operations to be performed aim to transform a flat table into a ROLAP (Relational On-Line Analytical Processing) star database. The main objective of the package is to allow the definition of these transformations easily. The implementation of the multidimensional database obtained can be exported to work with multidimensional analysis tools on spreadsheets or relational databases.
Maintained by Jose Samos. Last updated 1 years ago.
46.9 match 5 stars 6.12 score 25 scripts 1 dependentsmicrosoft
wpa:Tools for Analysing and Visualising Viva Insights Data
Opinionated functions that enable easier and faster analysis of Viva Insights data. There are three main types of functions in 'wpa': (i) Standard functions create a 'ggplot' visual or a summary table based on a specific Viva Insights metric; (2) Report Generation functions generate HTML reports on a specific analysis area, e.g. Collaboration; (3) Other miscellaneous functions cover more specific applications (e.g. Subject Line text mining) of Viva Insights data. This package adheres to 'tidyverse' principles and works well with the pipe syntax. 'wpa' is built with the beginner-to-intermediate R users in mind, and is optimised for simplicity.
Maintained by Martin Chan. Last updated 4 months ago.
41.9 match 30 stars 6.69 score 39 scripts 1 dependentsigraph
igraph:Network Analysis and Visualization
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Maintained by Kirill Mรผller. Last updated 14 hours ago.
complex-networksgraph-algorithmsgraph-theorymathematicsnetwork-analysisnetwork-graphfortranlibxml2glpkopenblascpp
12.0 match 582 stars 21.11 score 31k scripts 1.9k dependentsr-spatial
sf:Simple Features for R
Support for simple feature access, a standardized way to encode and analyze spatial vector data. Binds to 'GDAL' <doi: 10.5281/zenodo.5884351> for reading and writing data, to 'GEOS' <doi: 10.5281/zenodo.11396894> for geometrical operations, and to 'PROJ' <doi: 10.5281/zenodo.5884394> for projection conversions and datum transformations. Uses by default the 's2' package for geometry operations on geodetic (long/lat degree) coordinates.
Maintained by Edzer Pebesma. Last updated 17 days ago.
11.3 match 1.4k stars 22.42 score 117k scripts 1.2k dependentsrspatial
terra:Spatial Data Analysis
Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Maintained by Robert J. Hijmans. Last updated 19 hours ago.
geospatialrasterspatialvectoronetbbprojgdalgeoscpp
14.3 match 559 stars 17.64 score 17k scripts 851 dependentsappelmar
gdalcubes:Earth Observation Data Cubes from Satellite Image Collections
Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, plotting, and extraction from spatial and or spatiotemporal features. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Maintained by Marius Appel. Last updated 1 years ago.
remote-sensingsatellite-imageryspatial-analysisgdalnetcdfcpp
30.0 match 124 stars 8.39 score 356 scriptsmrc-ide
dust2:Next Generation dust
Experimental sources for the next generation of dust, which will properly adopt the particle filter, have support for partial parameter updates, support for multiple parameter sets and hopefully better GPU/MPI support.
Maintained by Rich FitzJohn. Last updated 11 days ago.
36.4 match 6.66 score 32 scripts 2 dependentsaphalo
photobiology:Photobiological Calculations
Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Maintained by Pedro J. Aphalo. Last updated 4 days ago.
lightphotobiologyquantificationr4photobiology-suiteradiationspectrasun-position
25.8 match 4 stars 9.35 score 604 scripts 12 dependentsdankelley
oce:Analysis of Oceanographic Data
Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.
Maintained by Dan Kelley. Last updated 2 days ago.
15.5 match 146 stars 15.42 score 4.2k scripts 18 dependentsbioc
GenomicDataCommons:NIH / NCI Genomic Data Commons Access
Programmatically access the NIH / NCI Genomic Data Commons RESTful service.
Maintained by Sean Davis. Last updated 1 months ago.
dataimportsequencingapi-clientbioconductorbioinformaticscancercore-servicesdata-sciencegenomicsncitcgavignette
19.7 match 87 stars 11.94 score 238 scripts 12 dependentsinbo
inbodb:Connect to and Retrieve Data from Databases on the INBO Server
A bundle of functions to connect to and retrieve data from databases on the INBO server, with dedicated functions to query some of these databases.
Maintained by Els Lommelen. Last updated 26 days ago.
37.4 match 6.16 score 114 scripts 1 dependentsjohn-harrold
ubiquity:PKPD, PBPK, and Systems Pharmacology Modeling Tools
Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.
Maintained by John Harrold. Last updated 18 days ago.
31.2 match 13 stars 7.14 score 33 scriptspedrocoutinhosilva
imola:CSS Layouts (Grid and Flexbox) Implementation for R/Shiny
Allows easy creation of CSS layouts (grid and flexbox) directly from R without added CSS.
Maintained by Pedro Silva. Last updated 1 years ago.
30.5 match 75 stars 6.94 score 33 scriptsr-lib
systemfonts:System Native Font Finding
Provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts across different operating systems. The 'systemfonts' package provides bindings to the native libraries on Windows, macOS and Linux for finding font files that can then be used further by e.g. graphic devices. The main use is intended to be from compiled code but 'systemfonts' also provides access from R.
Maintained by Thomas Lin Pedersen. Last updated 2 months ago.
13.3 match 95 stars 15.62 score 384 scripts 990 dependentsbenubah
control:A Control Systems Toolbox
Solves control systems problems relating to time/frequency response, LTI systems design and analysis, transfer function manipulations, and system conversion.
Maintained by Ben C. Ubah. Last updated 5 years ago.
35.3 match 19 stars 5.86 score 76 scriptsflippiecoetser
Query:Write SQL Statements with ease
This package provides a set of utility functions to efficiently write SQL Statements: In essence converting R to SQL.
Maintained by Flippie Coetser. Last updated 1 years ago.
52.0 match 2 stars 3.73 score 179 scripts 1 dependentssvmiller
peacesciencer:Tools and Data for Quantitative Peace Science Research
These are useful tools and data sets for the study of quantitative peace science. The goal for this package is to include tools and data sets for doing original research that mimics well what a user would have to previously get from a software package that may not be well-sourced or well-supported. Those software bundles were useful the extent to which they encourage replications of long-standing analyses by starting the data-generating process from scratch. However, a lot of the functionality can be done relatively quickly and more transparently in the R programming language.
Maintained by Steve Miller. Last updated 4 days ago.
35.1 match 29 stars 5.49 score 211 scriptstudo-r
BatchJobs:Batch Computing with R
Provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported. For further details see the project web page.
Maintained by Bernd Bischl. Last updated 3 years ago.
22.3 match 85 stars 8.57 score 616 scripts 3 dependentsr-lib
desc:Manipulate DESCRIPTION Files
Tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.
Maintained by Gรกbor Csรกrdi. Last updated 1 months ago.
12.9 match 123 stars 14.68 score 409 scripts 1.1k dependentsr-lib
fs:Cross-Platform File System Operations Based on 'libuv'
A cross-platform interface to file system operations, built on top of the 'libuv' C library.
Maintained by Gรกbor Csรกrdi. Last updated 4 months ago.
9.2 match 370 stars 20.26 score 8.1k scripts 5.2k dependentsgreat-northern-diver
loon:Interactive Statistical Data Visualization
An extendable toolkit for interactive data visualization and exploration.
Maintained by R. Wayne Oldford. Last updated 2 years ago.
data-analysisdata-sciencedata-visualizationexploratory-analysisexploratory-data-analysishigh-dimensional-datainteractive-graphicsinteractive-visualizationsloonpythonstatistical-analysisstatistical-graphicsstatisticstcl-extensiontk
20.6 match 48 stars 9.00 score 93 scripts 5 dependentsdwulff
text2sdg:Detecting UN Sustainable Development Goals in Text
The United Nationsโ Sustainable Development Goals (SDGs) have become an important guideline for organisations to monitor and plan their contributions to social, economic, and environmental transformations. The 'text2sdg' package is an open-source analysis package that identifies SDGs in text using scientifically developed query systems, opening up the opportunity to monitor any type of text-based data, such as scientific output or corporate publications. For more information regarding the methodology see Meier, Mata & Wulff (2022) <arXiv:2110.05856>.
Maintained by Dominik S. Meier. Last updated 6 months ago.
natural-language-processingsustainabilitysustainable-developmentsustainable-development-goals
28.8 match 18 stars 6.13 score 9 scriptsjpgattuso
seacarb:Seawater Carbonate Chemistry
Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Maintained by Jean-Pierre Gattuso. Last updated 1 years ago.
21.3 match 8 stars 8.27 score 350 scripts 5 dependentseguidotti
calculus:High Dimensional Numerical and Symbolic Calculus
Efficient C++ optimized functions for numerical and symbolic calculus as described in Guidotti (2022) <doi:10.18637/jss.v104.i05>. It includes basic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, high-order derivatives, ordinary differential equations, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.
Maintained by Emanuele Guidotti. Last updated 2 years ago.
calculuscoordinate-systemscurldivergenceeinsteinfinite-differencegradienthermitehessianjacobianlaplaciannumerical-derivationnumerical-derivativesnumerical-differentiationsymbolic-computationsymbolic-differentiationtaylorcpp
19.7 match 47 stars 8.92 score 66 scripts 7 dependentscbiit
LDlinkR:Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest
Provides access to the 'LDlink' API (<https://ldlink.nih.gov/?tab=apiaccess>) using the R console. This programmatic access facilitates researchers who are interested in performing batch queries in 1000 Genomes Project (2015) <doi:10.1038/nature15393> data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying germline variants in human population groups of interest. For more details, please see Machiela et al. (2015) <doi:10.1093/bioinformatics/btv402>.
Maintained by Timothy A. Myers. Last updated 11 months ago.
ld-calculatorldlinkldlink-apildlink-webtoollinkage-disequilibriumpopulation-genetics
18.8 match 58 stars 9.21 score 206 scripts 1 dependentsbemts-hhs
nemsqar:National Emergency Medical Service Quality Alliance Measure Calculations
Designed to automate the calculation of Emergency Medical Service (EMS) quality metrics, 'nemsqar' implements measures defined by the National EMS Quality Alliance (NEMSQA). By providing reliable, evidence-based quality assessments, the package supports EMS agencies, healthcare providers, and researchers in evaluating and improving patient outcomes. Users can find details on all approved NEMSQA measures at <https://www.nemsqa.org/measures>. Full technical specifications, including documentation and pseudocode used to develop 'nemsqar', are available on the NEMSQA website after creating a user profile at <https://www.nemsqa.org>.
Maintained by Nicolas Foss. Last updated 4 days ago.
36.5 match 5 stars 4.70 scoremrc-ide
orderly2:Orderly Next Generation
Distributed reproducible computing framework, adopting ideas from git, docker and other software. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.
Maintained by Rich FitzJohn. Last updated 2 months ago.
20.6 match 8 stars 8.30 score 49 scripts 2 dependentscivisanalytics
civis:R Client for the 'Civis Platform API'
A convenient interface for making requests directly to the 'Civis Platform API' <https://www.civisanalytics.com/platform/>. Full documentation available 'here' <https://civisanalytics.github.io/civis-r/>.
Maintained by Peter Cooman. Last updated 2 months ago.
21.6 match 16 stars 7.84 score 144 scriptskasperwelbers
corpustools:Managing, Querying and Analyzing Tokenized Text
Provides text analysis in R, focusing on the use of a tokenized text format. In this format, the positions of tokens are maintained, and each token can be annotated (e.g., part-of-speech tags, dependency relations). Prominent features include advanced Lucene-like querying for specific tokens or contexts (e.g., documents, sentences), similarity statistics for words and documents, exporting to DTM for compatibility with many text analysis packages, and the possibility to reconstruct original text from tokens to facilitate interpretation.
Maintained by Kasper Welbers. Last updated 6 months ago.
22.5 match 31 stars 7.50 score 174 scripts 1 dependentssteffenmoritz
imputeTS:Time Series Missing Value Imputation
Imputation (replacement) of missing values in univariate time series. Offers several imputation functions and missing data plots. Available imputation algorithms include: 'Mean', 'LOCF', 'Interpolation', 'Moving Average', 'Seasonal Decomposition', 'Kalman Smoothing on Structural Time Series models', 'Kalman Smoothing on ARIMA models'. Published in Moritz and Bartz-Beielstein (2017) <doi:10.32614/RJ-2017-009>.
Maintained by Steffen Moritz. Last updated 3 years ago.
data-visualizationimputationimputation-algorithmimputetsmissing-datatime-seriescpp
13.7 match 162 stars 12.18 score 1.9k scripts 27 dependentsintegrated-inferences
CausalQueries:Make, Update, and Query Binary Causal Models
Users can declare causal models over binary nodes, update beliefs about causal types given data, and calculate arbitrary queries. Updating is implemented in 'stan'. See Humphreys and Jacobs, 2023, Integrated Inferences (<DOI: 10.1017/9781316718636>) and Pearl, 2009 Causality (<DOI:10.1017/CBO9780511803161>).
Maintained by Till Tietz. Last updated 24 days ago.
bayescausaldagsmixedmethodsstancpp
18.2 match 27 stars 9.03 score 54 scriptsjessecambon
tidygeocoder:Geocoding Made Easy
An intuitive interface for getting data from geocoding services.
Maintained by Jesse Cambon. Last updated 4 months ago.
13.9 match 287 stars 11.35 score 1.0k scripts 9 dependentsmrcieu
gwasvcf:Tools for Dealing with GWAS Summary Data in VCF Format
Tools for dealing with GWAS summary data in VCF format. Includes reading, querying, writing, as well as helper functions such as LD proxy searches.
Maintained by Gibran Hemani. Last updated 2 years ago.
27.9 match 77 stars 5.65 score 129 scripts 1 dependentsropensci
biomartr:Genomic Data Retrieval
Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.
Maintained by Hajk-Georg Drost. Last updated 1 months ago.
biomartgenomic-data-retrievalannotation-retrievaldatabase-retrievalncbiensemblbiological-data-retrievalensembl-serversgenomegenome-annotationgenome-retrievalgenomicsmeta-analysismetagenomicsncbi-genbankpeer-reviewedproteomesequenced-genomes
13.8 match 218 stars 11.35 score 129 scripts 3 dependentsbioc
annotate:Annotation for microarrays
Using R enviroments for annotation.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
13.6 match 11.41 score 812 scripts 243 dependentsbioc
GenomicDistributions:GenomicDistributions: fast analysis of genomic intervals with Bioconductor
If you have a set of genomic ranges, this package can help you with visualization and comparison. It produces several kinds of plots, for example: Chromosome distribution plots, which visualize how your regions are distributed over chromosomes; feature distance distribution plots, which visualizes how your regions are distributed relative to a feature of interest, like Transcription Start Sites (TSSs); genomic partition plots, which visualize how your regions overlap given genomic features such as promoters, introns, exons, or intergenic regions. It also makes it easy to compare one set of ranges to another.
Maintained by Kristyna Kupkova. Last updated 5 months ago.
softwaregenomeannotationgenomeassemblydatarepresentationsequencingcoveragefunctionalgenomicsvisualization
20.9 match 26 stars 7.44 score 25 scriptsdarwin-eu
PatientProfiles:Identify Characteristics of Patients in the OMOP Common Data Model
Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Maintained by Marti Catala. Last updated 10 days ago.
15.3 match 1 stars 9.97 score 225 scripts 9 dependentsdoi-usgs
sbtools:USGS ScienceBase Tools
Tools for interacting with U.S. Geological Survey ScienceBase <https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and collaborative data management platform. Functions included for querying ScienceBase, and creating and fetching datasets.
Maintained by David Blodgett. Last updated 10 months ago.
18.7 match 21 stars 7.94 score 127 scripts 2 dependentsoscarperpinan
solaR:Radiation and Photovoltaic Systems
Calculation methods of solar radiation and performance of photovoltaic systems from daily and intradaily irradiation data sources.
Maintained by Oscar Perpiรฑรกn Lamigueiro. Last updated 26 days ago.
28.0 match 38 stars 5.32 score 55 scriptsbioc
OncoScore:A tool to identify potentially oncogenic genes
OncoScore is a tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries.
Maintained by Luca De Sano. Last updated 5 months ago.
24.1 match 5 stars 6.15 score 2 scriptsbioc
loci2path:Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
loci2path performs statistics-rigorous enrichment analysis of eQTLs in genomic regions of interest. Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB.
Maintained by Tianlei Xu. Last updated 5 months ago.
functionalgenomicsgeneticsgenesetenrichmentsoftwaregeneexpressionsequencingcoveragebiocarta
34.3 match 1 stars 4.30 score 2 scriptspaws-r
paws:Amazon Web Services Software Development Kit
Interface to Amazon Web Services <https://aws.amazon.com>, including storage, database, and compute services, such as 'Simple Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda' functions-as-a-service.
Maintained by Dyfan Jones. Last updated 5 days ago.
13.0 match 332 stars 11.25 score 177 scripts 12 dependentspolmine
polmineR:Verbs and Nouns for Corpus Analysis
Package for corpus analysis using the Corpus Workbench ('CWB', <https://cwb.sourceforge.io>) as an efficient back end for indexing and querying large corpora. The package offers functionality to flexibly create subcorpora and to carry out basic statistical operations (count, co-occurrences etc.). The original full text of documents can be reconstructed and inspected at any time. Beyond that, the package is intended to serve as an interface to packages implementing advanced statistical procedures. Respective data structures (document-term matrices, term-co-occurrence matrices etc.) can be created based on the indexed corpora.
Maintained by Andreas Blaette. Last updated 1 years ago.
18.3 match 49 stars 7.96 score 311 scriptsmgondan
rolog:Query 'SWI'-'Prolog' from R
This R package connects to SWI-Prolog, <https://www.swi-prolog.org/>, so that R can send deterministic and non-deterministic queries to prolog (consult, query/submit, once, findall).
Maintained by Matthias Gondan. Last updated 7 days ago.
22.8 match 4 stars 6.37 score 10 scripts 1 dependentsrblp
Rblpapi:R Interface to 'Bloomberg'
An R Interface to 'Bloomberg' is provided via the 'Blp API'.
Maintained by Dirk Eddelbuettel. Last updated 1 days ago.
15.4 match 169 stars 9.41 score 115 scriptsr-lib
pkgdepends:Package Dependency Resolution and Downloads
Find recursive dependencies of 'R' packages from various sources. Solve the dependencies to obtain a consistent set of packages to install. Download packages, and install them. It supports packages on 'CRAN', 'Bioconductor' and other 'CRAN-like' repositories, 'GitHub', package 'URLs', and local package trees and files. It caches metadata and package files via the 'pkgcache' package, and performs all 'HTTP' requests, downloads, builds and installations in parallel. 'pkgdepends' is the workhorse of the 'pak' package.
Maintained by Gรกbor Csรกrdi. Last updated 18 days ago.
14.4 match 110 stars 9.89 score 67 scripts 5 dependentswinvector
rquery:Relational Query Generator for Data Manipulation at Scale
A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible table modeling step, plus explicit query reasoning and checking.
Maintained by John Mount. Last updated 2 years ago.
14.9 match 110 stars 9.53 score 126 scripts 3 dependentsluukvdmeer
sfnetworks:Tidy Geospatial Networks
Provides a tidy approach to spatial network analysis, in the form of classes and functions that enable a seamless interaction between the network analysis package 'tidygraph' and the spatial analysis package 'sf'.
Maintained by Lucas van der Meer. Last updated 3 months ago.
geospatial-networksnetwork-analysisrspatialsimple-featuresspatial-analysisspatial-data-sciencespatial-networkstidygraphtidyverse
14.8 match 372 stars 9.63 score 332 scripts 6 dependentsgagolews
stringi:Fast and Portable Character String Processing Facilities
A collection of character string/text/natural language processing tools for pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date-time formatting and parsing, and many more. They are fast, consistent, convenient, and - thanks to 'ICU' (International Components for Unicode) - portable across all locales and platforms. Documentation about 'stringi' is provided via its website at <https://stringi.gagolewski.com/> and the paper by Gagolewski (2022, <doi:10.18637/jss.v103.i02>).
Maintained by Marek Gagolewski. Last updated 1 months ago.
icuicu4cnatural-language-processingnlpregexregexpstring-manipulationstringistringrtexttext-processingtidy-dataunicodecpp
7.8 match 309 stars 18.31 score 10k scripts 8.6k dependentslouisaslett
ReliabilityTheory:Structural Reliability Analysis
Perform structural reliability analysis, including computation and simulation with system signatures, Samaniego (2007) <doi:10.1007/978-0-387-71797-5>, and survival signatures, Coolen and Coolen-Maturi (2013) <doi:10.1007/978-3-642-30662-4_8>. Additionally supports parametric and topological inference given system lifetime data, Aslett (2012) <https://www.louisaslett.com/PhD_Thesis.pdf>.
Maintained by Louis Aslett. Last updated 6 months ago.
36.0 match 7 stars 3.92 score 12 scriptsmicrosoft
vivainsights:Analyze and Visualize Data from 'Microsoft Viva Insights'
Provides a versatile range of functions, including exploratory data analysis, time-series analysis, organizational network analysis, and data validation, whilst at the same time implements a set of best practices in analyzing and visualizing data specific to 'Microsoft Viva Insights'.
Maintained by Martin Chan. Last updated 25 days ago.
23.0 match 11 stars 6.12 score 68 scriptsncss-tech
soilDB:Soil Database Interface
A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Maintained by Andrew Brown. Last updated 8 days ago.
ksslnasisnrcssoilsoil-data-accesssoil-surveysoilwebsqlusda
12.3 match 87 stars 11.34 score 1.0k scripts 1 dependentsapache
apache.sedona:R Interface for Apache Sedona
R interface for 'Apache Sedona' based on 'sparklyr' (<https://sedona.apache.org>).
Maintained by Apache Sedona. Last updated 2 days ago.
cluster-computinggeospatialjavapythonscalaspatial-analysisspatial-queryspatial-sql
13.0 match 2.0k stars 10.72 score 105 scriptsyixuan
recosystem:Recommender System using Matrix Factorization
R wrapper of the 'libmf' library <https://www.csie.ntu.edu.tw/~cjlin/libmf/> for recommender system using matrix factorization. It is typically used to approximate an incomplete matrix using the product of two matrices in a latent space. Other common names for this task include "collaborative filtering", "matrix completion", "matrix recovery", etc. High performance multi-core parallel computing is supported in this package.
Maintained by Yixuan Qiu. Last updated 2 years ago.
matrix-factorizationrecommender-systemcppopenmp
17.0 match 84 stars 7.97 score 101 scripts 6 dependentscritical-infrastructure-systems-lab
ldsr:Linear Dynamical System Reconstruction
Streamflow (and climate) reconstruction using Linear Dynamical Systems. The advantage of this method is the additional state trajectory which can reveal more information about the catchment or climate system. For details of the method please refer to Nguyen and Galelli (2018) <doi:10.1002/2017WR022114>.
Maintained by Hung Nguyen. Last updated 5 years ago.
expectation-maximization-algorithmhydrologykalman-smootherlinear-dynamical-systemspaleoclimateopenblascppopenmp
27.8 match 8 stars 4.86 score 18 scriptsphippsy
brandwatchR:'Brandwatch' API to R
Interact with the 'Brandwatch' API <https://developers.brandwatch.com/docs>. Allows you to authenticate to the API and obtain data for projects, queries, query groups tags and categories. Also allows you to directly obtain mentions and aggregate data for a specified query or query group.
Maintained by Donal Phipps. Last updated 7 years ago.
31.9 match 11 stars 4.16 score 26 scriptswillgearty
deeptime:Plotting Tools for Anyone Working in Deep Time
Extends the functionality of other plotting packages (notably 'ggplot2') to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data. The primary goal of 'deeptime' is to enable users to add highly customizable timescales to their visualizations. Other functions are also included to assist with other areas of deep time visualization.
Maintained by William Gearty. Last updated 3 months ago.
geologyggplot2paleontologyvisualization
12.3 match 92 stars 10.61 score 207 scripts 3 dependentsusepa
tcpl:ToxCast Data Analysis Pipeline
The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.
Maintained by Jason Brown. Last updated 4 days ago.
13.7 match 36 stars 9.41 score 90 scriptsjosesamos
geomultistar:Multidimensional Queries Enriched with Geographic Data
Multidimensional systems allow complex queries to be carried out in an easy way. The geographical dimension, together with the temporal dimension, plays a fundamental role in multidimensional systems. Through this package, vector geographic data layers can be associated to the attributes of geographic dimensions, so that the results of multidimensional queries can be obtained directly as vector layers. The multidimensional structures on which we can define the queries can be created from a flat table or imported directly using functions from this package.
Maintained by Jose Samos. Last updated 8 months ago.
28.7 match 2 stars 4.48 score 8 scripts 1 dependentsmountainmath
cancensus:Access, Retrieve, and Work with Canadian Census Data and Geography
Integrated, convenient, and uniform access to Canadian Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready tidy data frames and spatial data in multiple formats, as well as convenience functions for working with Census variables, variable hierarchies, and region selection. API keys are freely available with free registration at <https://censusmapper.ca/api>. Census data and boundary geometries are reproduced and distributed on an "as is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006; 2011; 2016; 2021).
Maintained by Dmitry Shkolnik. Last updated 1 years ago.
14.0 match 82 stars 8.80 score 414 scriptsatlasoflivingaustralia
galah:Biodiversity Data from the GBIF Node Network
The Global Biodiversity Information Facility ('GBIF', <https://www.gbif.org>) sources data from an international network of data providers, known as 'nodes'. Several of these nodes - the "living atlases" (<https://living-atlases.gbif.org>) - maintain their own web services using software originally developed by the Atlas of Living Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community to directly access data and resources hosted by 'GBIF' and its partner nodes.
Maintained by Martin Westgate. Last updated 1 months ago.
13.4 match 43 stars 9.17 score 275 scripts 1 dependentsidigbio
ridigbio:Interface to the iDigBio Data API
An interface to iDigBio's search API that allows downloading specimen records. Searches are returned as a data.frame. Other functions such as the metadata end points return lists of information. iDigBio is a US project focused on digitizing and serving museum specimen collections on the web. See <https://www.idigbio.org> for information on iDigBio.
Maintained by Jesse Bennett. Last updated 6 days ago.
12.0 match 16 stars 10.23 score 63 scripts 7 dependentsopenintrostat
openintro:Datasets and Supplemental Functions from 'OpenIntro' Textbooks and Labs
Supplemental functions and data for 'OpenIntro' resources, which includes open-source textbooks and resources for introductory statistics (<https://www.openintro.org/>). The package contains datasets used in our open-source textbooks along with custom plotting functions for reproducing book figures. Note that many functions and examples include color transparency; some plotting elements may not show up properly (or at all) when run in some versions of Windows operating system.
Maintained by Mine รetinkaya-Rundel. Last updated 3 months ago.
10.6 match 240 stars 11.39 score 6.0k scriptsropensci
bikedata:Download and Aggregate Data from Public Hire Bicycle Systems
Download and aggregate data from all public hire bicycle systems which provide open data, currently including 'Santander' Cycles in London, U.K.; from the U.S.A., 'Ford GoBike' in San Francisco CA, 'citibike' in New York City NY, 'Divvy' in Chicago IL, 'Capital Bikeshare' in Washington DC, 'Hubway' in Boston MA, 'Metro' in Los Angeles LA, 'Indego' in Philadelphia PA, and 'Nice Ride' in Minnesota; 'Bixi' from Montreal, Canada; and 'mibici' from Guadalajara, Mexico.
Maintained by Mark Padgham. Last updated 1 years ago.
bicycle-hire-systemsbike-hire-systemsbike-hirebicycle-hiredatabasebike-datapeer-reviewedcpp
20.2 match 83 stars 5.97 score 28 scriptsconstantino-garcia
nonlinearTseries:Nonlinear Time Series Analysis
Functions for nonlinear time series analysis. This package permits the computation of the most-used nonlinear statistics/algorithms including generalized correlation dimension, information dimension, largest Lyapunov exponent, sample entropy and Recurrence Quantification Analysis (RQA), among others. Basic routines for surrogate data testing are also included. Part of this work was based on the book "Nonlinear time series analysis" by Holger Kantz and Thomas Schreiber (ISBN: 9780521529020).
Maintained by Constantino A. Garcia. Last updated 6 months ago.
chaoschaotic-systemsnonlinear-dynamicsnonlinear-time-seriestime-seriesopenblascpp
13.3 match 35 stars 8.98 score 123 scripts 7 dependentsianmcook
tidyquery:Query 'R' Data Frames with 'SQL'
Use 'SQL' 'SELECT' statements to query 'R' data frames.
Maintained by Ian Cook. Last updated 2 years ago.
20.1 match 168 stars 5.95 score 35 scriptsthomasp85
tidygraph:A Tidy API for Graph Manipulation
A graph, while not "tidy" in itself, can be thought of as two tidy data frames describing node and edge data respectively. 'tidygraph' provides an approach to manipulate these two virtual data frames using the API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms.
Maintained by Thomas Lin Pedersen. Last updated 1 months ago.
graph-algorithmsgraph-manipulationigraphnetwork-analysistidyversecpp
8.0 match 553 stars 14.74 score 4.6k scripts 136 dependentsbioc
TCGAbiolinks:TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.
Maintained by Tiago Chedraoui Silva. Last updated 28 days ago.
dnamethylationdifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetworksequencingsurvivalsoftwarebiocbioconductorgdcintegrative-analysistcgatcga-datatcgabiolinks
8.0 match 305 stars 14.45 score 1.6k scripts 6 dependentssolarization
solaR2:Radiation and Photovoltaic Systems
Provides tools for calculating solar geometry, solar radiation on horizontal and inclined planes, and simulating the performance of various photovoltaic (PV) systems. Supports daily and intradaily irradiation data, enabling detailed analysis of grid-connected and water-pumping PV systems, including shading effects and solar angle calculations.
Maintained by Francisco Delgado-Lรณpez. Last updated 26 days ago.
28.2 match 1 stars 4.08 score 5 scriptsr-forge
systemfit:Estimating Systems of Simultaneous Equations
Econometric estimation of simultaneous systems of linear and nonlinear equations using Ordinary Least Squares (OLS), Weighted Least Squares (WLS), Seemingly Unrelated Regressions (SUR), Two-Stage Least Squares (2SLS), Weighted Two-Stage Least Squares (W2SLS), and Three-Stage Least Squares (3SLS) as suggested, e.g., by Zellner (1962) <doi:10.2307/2281644>, Zellner and Theil (1962) <doi:10.2307/1911287>, and Schmidt (1990) <doi:10.1016/0304-4076(90)90127-F>.
Maintained by Arne Henningsen. Last updated 2 years ago.
13.0 match 8.81 score 484 scripts 20 dependentsazure
AzureKusto:Interface to 'Kusto'/'Azure Data Explorer'
An interface to 'Azure Data Explorer', also known as 'Kusto', a fast, distributed data exploration service from Microsoft: <https://azure.microsoft.com/en-us/products/data-explorer/>. Includes 'DBI' and 'dplyr' interfaces, with the latter modelled after the 'dbplyr' package, whereby queries are translated from R into the native 'KQL' query language and executed lazily. On the admin side, the package extends the object framework provided by 'AzureRMR' to support creation and deletion of databases, and management of database principals. Part of the 'AzureR' family of packages.
Maintained by Alex Kyllo. Last updated 1 years ago.
azureazure-data-explorerazure-sdk-rbig-data-analyticskusto
22.0 match 18 stars 5.19 score 9 scriptsrdatatable
data.table:Extension of `data.frame`
Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Maintained by Tyson Barrett. Last updated 13 hours ago.
4.8 match 3.7k stars 23.53 score 230k scripts 4.6k dependentsjlmelville
rnndescent:Nearest Neighbor Descent Method for Approximate Nearest Neighbors
The Nearest Neighbor Descent method for finding approximate nearest neighbors by Dong and co-workers (2010) <doi:10.1145/1963405.1963487>. Based on the 'Python' package 'PyNNDescent' <https://github.com/lmcinnes/pynndescent>.
Maintained by James Melville. Last updated 8 months ago.
approximate-nearest-neighbor-searchcpp
15.4 match 11 stars 7.31 score 75 scriptstalgalili
installr:Using R to Install Stuff on Windows OS (Such As: R, 'Rtools', 'RStudio', 'Git', and More!)
R is great for installing software. Through the 'installr' package you can automate the updating of R (on Windows, using updateR()) and install new software. Software installation is initiated through a GUI (just run installr()), or through functions such as: install.Rtools(), install.pandoc(), install.git(), and many more. The updateR() command performs the following: finding the latest R version, downloading it, running the installer, deleting the installation file, copy and updating old packages to the new R installation.
Maintained by Tal Galili. Last updated 1 years ago.
11.1 match 273 stars 10.19 score 1.2k scriptsr-lib
pkgcache:Cache 'CRAN'-Like Metadata and R Packages
Metadata and package cache for CRAN-like repositories. This is a utility package to be used by package management tools that want to take advantage of caching.
Maintained by Gรกbor Csรกrdi. Last updated 18 days ago.
12.6 match 28 stars 8.85 score 31 scripts 6 dependentsropensci
rix:Reproducible Data Science Environments with 'Nix'
Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.
Maintained by Bruno Rodrigues. Last updated 10 hours ago.
nixpeer-reviewedreproducibilityreproducible-research
10.4 match 238 stars 10.55 score 67 scriptsbioc
scDiagnostics:Cell type annotation diagnostics
The scDiagnostics package provides diagnostic plots to assess the quality of cell type assignments from single cell gene expression profiles. The implemented functionality allows to assess the reliability of cell type annotations, investigate gene expression patterns, and explore relationships between different cell types in query and reference datasets allowing users to detect potential misalignments between reference and query datasets. The package also provides visualization capabilities for diagnostics purposes.
Maintained by Anthony Christidis. Last updated 5 months ago.
annotationclassificationclusteringgeneexpressionrnaseqsinglecellsoftwaretranscriptomics
14.0 match 8 stars 7.77 score 46 scriptstobiste
tectonicr:Analyzing the Orientation of Maximum Horizontal Stress
Models the direction of the maximum horizontal stress using relative plate motion parameters. Statistical algorithms to evaluate the modeling results compared with the observed data. Provides plots to visualize the results. Methods described in Stephan et al. (2023) <doi:10.1038/s41598-023-42433-2> and Wdowinski (1998) <doi:10.1016/S0079-1946(98)00091-3>.
Maintained by Tobias Stephan. Last updated 15 days ago.
geologystructural-geologytectonics
14.9 match 7 stars 7.26 score 33 scriptsbioc
snapcount:R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
snapcount is a client interface to the Snaptron webservices which support querying by gene name or genomic region. Results include raw expression counts derived from alignment of RNA-seq samples and/or various summarized measures of expression across one or more regions/genes per-sample (e.g. percent spliced in).
Maintained by Rone Charles. Last updated 5 months ago.
coveragegeneexpressionrnaseqsequencingsoftwaredataimport
20.4 match 3 stars 5.19 score 13 scriptsmdlincoln
clipr:Read and Write from the System Clipboard
Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.
Maintained by Matthew Lincoln. Last updated 3 years ago.
6.9 match 151 stars 15.21 score 608 scripts 2.4k dependentsgroditi
blsR:Make Requests from the Bureau of Labor Statistics API
Implements v2 of the B.L.S. API for requests of survey information and time series data through 3-tiered API that allows users to interact with the raw API directly, create queries through a functional interface, and re-shape the data structures returned to fit common uses. The API definition is located at: <https://www.bls.gov/developers/api_signature_v2.htm>.
Maintained by Guillermo Roditi Dominguez. Last updated 1 years ago.
23.4 match 14 stars 4.45 score 40 scriptstidyverse
dbplyr:A 'dplyr' Back End for Databases
A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.
Maintained by Hadley Wickham. Last updated 3 months ago.
5.3 match 481 stars 19.72 score 5.2k scripts 736 dependentscjbarrie
academictwitteR:Access the Twitter Academic Research Product Track V2 API Endpoint
Package to query the Twitter Academic Research Product Track, providing access to full-archive search and other v2 API endpoints. Functions are written with academic research in mind. They provide flexibility in how the user wishes to store collected data, and encourage regular storage of data to mitigate loss when collecting large volumes of tweets. They also provide workarounds to manage and reshape the format in which data is provided on the client side.
Maintained by Christopher Barrie. Last updated 2 years ago.
11.4 match 275 stars 8.94 score 177 scriptsmelff
memisc:Management of Survey Data and Presentation of Analysis Results
An infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) 'SPSS' and 'Stata' files is provided. Further, the package allows to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to 'LaTeX' and HTML.
Maintained by Martin Elff. Last updated 12 days ago.
8.3 match 46 stars 12.34 score 1.2k scripts 13 dependentsr-dbi
RSQLite:SQLite Interface for R
Embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine and for various extensions in a recent version is included. System libraries will never be consulted because this package relies on static linking for the plugins it includes; this also ensures a consistent experience across all installations.
Maintained by Kirill Mรผller. Last updated 26 days ago.
5.3 match 327 stars 18.73 score 8.1k scripts 1.1k dependentsskoval
RISmed:Download Content from NCBI Databases
A set of tools to extract bibliographic content from the National Center for Biotechnology Information (NCBI) databases, including PubMed. The name RISmed is a portmanteau of RIS (for Research Information Systems, a common tag format for bibliographic data) and PubMed.
Maintained by Stephanie Kovalchik. Last updated 3 years ago.
14.4 match 38 stars 6.94 score 252 scripts 3 dependentsshichenxie
pedquant:Public Economic Data and Quantitative Analysis
Provides an interface to access public economic and financial data for economic research and quantitative analysis. The data sources including NBS, FRED, Sina, Eastmoney and etc. It also provides quantitative functions for trading strategies based on the 'data.table', 'TTR', 'PerformanceAnalytics' and etc packages.
Maintained by Shichen Xie. Last updated 3 days ago.
17.3 match 59 stars 5.70 score 34 scriptspik-piam
mredgebuildings:Prepare data to be used by the EDGE-Buildings model
Prepare data to be used by the EDGE-Buildings model.
Maintained by Robin Hasse. Last updated 3 days ago.
26.2 match 3.72 scorejandraor
readsdr:Translate Models from System Dynamics Software into 'R'
The goal of 'readsdr' is to bridge the design capabilities from specialised System Dynamics software with the powerful numerical tools offered by 'R' libraries. The package accomplishes this goal by parsing 'XMILE' files ('Vensim' and 'Stella') models into 'R' objects to construct networks (graph theory); 'ODE' functions for 'Stan'; and inputs to simulate via 'deSolve' as described in Duggan (2016) <doi:10.1007/978-3-319-34043-2>.
Maintained by Jair Andrade. Last updated 10 months ago.
14.6 match 19 stars 6.62 score 62 scriptsbioc
RCAS:RNA Centric Annotation System
RCAS is an R/Bioconductor package designed as a generic reporting tool for the functional analysis of transcriptome-wide regions of interest detected by high-throughput experiments. Such transcriptomic regions could be, for instance, signal peaks detected by CLIP-Seq analysis for protein-RNA interaction sites, RNA modification sites (alias the epitranscriptome), CAGE-tag locations, or any other collection of query regions at the level of the transcriptome. RCAS produces in-depth annotation summaries and coverage profiles based on the distribution of the query regions with respect to transcript features (exons, introns, 5'/3' UTR regions, exon-intron boundaries, promoter regions). Moreover, RCAS can carry out functional enrichment analyses and discriminative motif discovery.
Maintained by Bora Uyar. Last updated 5 months ago.
softwaregenetargetmotifannotationmotifdiscoverygotranscriptomicsgenomeannotationgenesetenrichmentcoverage
15.1 match 6.32 score 29 scripts 1 dependentskingaa
pomp:Statistical Inference for Partially Observed Markov Processes
Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Maintained by Aaron A. King. Last updated 1 months ago.
abcb-splinedifferential-equationsdynamical-systemsiterated-filteringlikelihoodlikelihood-freemarkov-chain-monte-carlomarkov-modelmathematical-modellingmeasurement-errorparticle-filtersequential-monte-carlosimulation-based-inferencesobol-sequencestate-spacestatistical-inferencestochastic-processestime-seriesopenblas
8.0 match 115 stars 11.81 score 1.3k scripts 4 dependentsobiba
opalr:'Opal' Data Repository Client and 'DataSHIELD' Utils
Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.
Maintained by Yannick Marcon. Last updated 2 months ago.
12.1 match 3 stars 7.76 score 179 scripts 2 dependentsropensci
rredlist:'IUCN' Red List Client
'IUCN' Red List (<https://api.iucnredlist.org/>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.
Maintained by William Gearty. Last updated 1 months ago.
iucnbiodiversityapiweb-servicestraitshabitatspeciesconservationapi-wrapperiucn-red-listtaxize
8.1 match 53 stars 11.49 score 195 scripts 24 dependentsdarwin-eu
CDMConnector:Connect to an OMOP Common Data Model
Provides tools for working with observational health data in the Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax. Common data model database table references are stored in a single compound object along with metadata.
Maintained by Adam Black. Last updated 19 days ago.
8.1 match 12 stars 11.39 score 502 scripts 12 dependentsdavid6marsh
himach:Find Routes for Supersonic Aircraft
For supersonic aircraft, flying subsonic over land, find the best route between airports. Allow for coastal buffer and potentially closed regions. Use a minimal model of aircraft performance: the focus is on time saved versus subsonic flight, rather than on vertical flight profile. For modelling and forecasting, not for planning your flight!
Maintained by David Marsh. Last updated 1 years ago.
22.9 match 1 stars 4.00 score 7 scriptsspectra-to-knowledge
SpectraToQueries:Spectra to queries
SpectraToQueries provides the infrastructure to translate spectra to queries.
Maintained by Adriano Rutz. Last updated 21 days ago.
knowledge extractionspectral informationquerying system
29.6 match 1 stars 3.02 scoreyihui
xfun:Supporting Functions for Packages Maintained by 'Yihui Xie'
Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Maintained by Yihui Xie. Last updated 4 days ago.
4.9 match 145 stars 18.18 score 916 scripts 4.4k dependentsdatawookie
emayili:Send Email Messages
A light, simple tool for sending emails with minimal dependencies.
Maintained by Andrew B. Collier. Last updated 1 months ago.
9.3 match 180 stars 9.59 score 95 scripts 3 dependentsalexpate30
rcprd:Extraction and Management of Clinical Practice Research Datalink Data
Simplify the process of extracting and processing Clinical Practice Research Datalink (CPRD) data in order to build datasets ready for statistical analysis. This process is difficult in 'R', as the raw data is very large and cannot be read into the R workspace. 'rcprd' utilises 'RSQLite' to create 'SQLite' databases which are stored on the hard disk. These are then queried to extract the required information for a cohort of interest, and create datasets ready for statistical analysis. The processes follow closely that from the 'rEHR' package, see Springate et al., (2017) <doi:10.1371/journal.pone.0171784>.
Maintained by Alexander Pate. Last updated 20 days ago.
16.2 match 2 stars 5.48 score 5 scriptsmrcieu
ieugwasr:Interface to the 'OpenGWAS' Database API
Interface to the 'OpenGWAS' database API <https://api.opengwas.io/api/>. Includes a wrapper to make generic calls to the API, plus convenience functions for specific queries.
Maintained by Gibran Hemani. Last updated 4 days ago.
8.2 match 89 stars 10.71 score 404 scripts 6 dependentsinlabru-org
fmesher:Triangle Meshes and Related Geometry Tools
Generate planar and spherical triangle meshes, compute finite element calculations for 1- and 2-dimensional flat and curved manifolds with associated basis function spaces, methods for lines and polygons, and transparent handling of coordinate reference systems and coordinate transformation, including 'sf' and 'sp' geometries. The core 'fmesher' library code was originally part of the 'INLA' package, and implements parts of "Triangulations and Applications" by Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.
Maintained by Finn Lindgren. Last updated 8 hours ago.
7.9 match 16 stars 11.20 score 261 scripts 26 dependentsdavisvaughan
treesitter:Bindings to 'Tree-Sitter'
Provides bindings to 'Tree-sitter', an incremental parsing system for programming tools. 'Tree-sitter' builds concrete syntax trees for source files of any language, and can efficiently update those syntax trees as the source file is edited. It also includes a robust error recovery system that provides useful parse results even in the presence of syntax errors.
Maintained by Davis Vaughan. Last updated 6 months ago.
13.3 match 37 stars 6.62 score 18 scripts 2 dependentsrfhb
ctrdata:Retrieve and Analyze Clinical Trials in 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'). 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 meta-analysis 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 2 days ago.
clinical-dataclinical-researchclinical-studiesclinical-trialsctgovdatabaseduckdbmongodbnodbipostgresqlregistersqlitestudiestrial
11.1 match 45 stars 7.92 score 32 scriptsips-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.
12.6 match 24 stars 6.89 score 135 scripts 1 dependentsnicolas-schmidt
esaps:Indicators of Electoral Systems and Party Systems
It allows structuring electoral data of different size and structure to calculate various indicators frequently used in the studies of electoral systems and party systems. Indicators of electoral volatility, electoral disproportionality, party nationalization and the effective number of parties are included.
Maintained by Nicolas Schmidt. Last updated 3 years ago.
electoral-systemsnationalization-scoreparty-nationalizationparty-systems
26.1 match 4 stars 3.30 score 5 scriptsbruigtp
REDCapDM:'REDCap' Data Management
REDCap Data Management - REDCapDM is an R package that allows users to manage data exported directly from REDCap or using an API connection. This package includes several functions designed for pre-processing data, generating reports of queries such as outliers or missing values, and following up on the identified queries. 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>) is a web application developed at Vanderbilt University, designed for creating and managing online surveys and databases and the REDCap API is an interface that allows external applications to connect to REDCap remotely, and is used to programmatically retrieve or modify project data or settings within REDCap, such as importing or exporting data.
Maintained by Joรฃo Carmezim. Last updated 3 days ago.
14.6 match 4 stars 5.89 score 9 scriptscran
BB:Solving and Optimizing Large-Scale Nonlinear Systems
Barzilai-Borwein spectral methods for solving nonlinear system of equations, and for optimizing nonlinear objective functions subject to simple constraints. A tutorial style introduction to this package is available in a vignette on the CRAN download page or, when the package is loaded in an R session, with vignette("BB").
Maintained by Paul Gilbert. Last updated 5 years ago.
13.1 match 2 stars 6.54 score 60 dependentsdmurdoch
rgl:3D Visualization Using OpenGL
Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Maintained by Duncan Murdoch. Last updated 2 months ago.
graphicsopenglrglwebgllibglulibglvndlibpnglibx11freetypecpp
4.9 match 91 stars 17.49 score 7.3k scripts 300 dependentselilillyco
rfacts:R Interface to 'FACTS' on Unix-Like Systems
The 'rfacts' package is an R interface to the Fixed and Adaptive Clinical Trial Simulator ('FACTS') on Unix-like systems. It programmatically invokes 'FACTS' to run clinical trial simulations, and it aggregates simulation output data into tidy data frames. These capabilities provide end-to-end automation for large-scale simulation pipelines, and they enhance computational reproducibility. For more information on 'FACTS' itself, please visit <https://www.berryconsultants.com/software/>.
Maintained by William Michael Landau. Last updated 3 years ago.
clinical-trialsfactssimulation
17.0 match 7 stars 5.02 score 10 scriptsbioc
recountmethylation:Access and analyze public DNA methylation array data compilations
Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.
Maintained by Sean K Maden. Last updated 5 months ago.
dnamethylationepigeneticsmicroarraymethylationarrayexperimenthub
13.6 match 9 stars 6.28 score 9 scriptsropensci
rnassqs:Access Data from the NASS 'Quick Stats' API
Interface to access data via the United States Department of Agriculture's National Agricultural Statistical Service (NASS) 'Quick Stats' web API <https://quickstats.nass.usda.gov/api/>. Convenience functions facilitate building queries based on available parameters and valid parameter values. This product uses the NASS API but is not endorsed or certified by NASS.
Maintained by Nicholas Potter. Last updated 7 months ago.
11.3 match 47 stars 7.49 score 63 scripts 1 dependentsthomasp85
shinyFiles:A Server-Side File System Viewer for Shiny
Provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to "download" files to a temporary location. Both file and folder selection as well as file saving is available.
Maintained by Thomas Lin Pedersen. Last updated 2 years ago.
7.2 match 199 stars 11.70 score 736 scripts 60 dependentsdami82
easyPubMed:Search and Retrieve Scientific Publication Records from PubMed
Query NCBI Entrez and retrieve PubMed records in XML or text format. Process PubMed records by extracting and aggregating data from selected fields. A large number of records can be easily downloaded via this simple-to-use interface to the NCBI PubMed API.
Maintained by Damiano Fantini. Last updated 1 years ago.
10.8 match 21 stars 7.83 score 178 scripts 4 dependentsmlverse
torch:Tensors and Neural Networks with 'GPU' Acceleration
Provides functionality to define and train neural networks similar to 'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R using the 'libtorch' library. Also supports low-level tensor operations and 'GPU' acceleration.
Maintained by Daniel Falbel. Last updated 7 days ago.
5.1 match 520 stars 16.52 score 1.4k scripts 38 dependentsms609
Ternary:Create Ternary and Holdridge Plots
Plots ternary diagrams (simplex plots / Gibbs triangles) and Holdridge life zone plots <doi:10.1126/science.105.2727.367> using the standard graphics functions. Allows custom annotation, interpolating, contouring and scaling of plotting region. Includes a 'Shiny' user interface for point-and-click ternary plotting. An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions.
Maintained by Martin R. Smith. Last updated 5 months ago.
graphicsplottingplotting-in-rternary-plots
8.8 match 33 stars 9.58 score 103 scripts 5 dependentsjpquast
protti:Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools
Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
Maintained by Jan-Philipp Quast. Last updated 5 months ago.
data-analysislip-msmass-spectrometryomicsproteinproteomicssystems-biology
9.8 match 61 stars 8.58 score 83 scriptshrbrmstr
sergeant:Tools to Transform and Query Data with Apache Drill
Apache Drill is a low-latency distributed query engine designed to enable data exploration and analysis on both relational and non-relational data stores, scaling to petabytes of data. Methods are provided that enable working with Apache Drill instances via the REST API, DBI methods and using 'dplyr'/'dbplyr' idioms. Helper functions are included to facilitate using official Drill Docker images/containers.
Maintained by Bob Rudis. Last updated 4 years ago.
24.2 match 3.45 score 56 scriptssimonpcouch
anyflights:Query 'nycflights13'-Like Air Travel Data for Given Years and Airports
Supplies a set of functions to query air travel data for user- specified years and airports. Datasets include on-time flights, airlines, airports, planes, and weather.
Maintained by Simon P. Couch. Last updated 2 months ago.
14.1 match 49 stars 5.90 score 23 scriptsbioc
biomaRt:Interface to BioMart databases (i.e. Ensembl)
In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<http://www.biomart.org>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.
Maintained by Mike Smith. Last updated 3 days ago.
annotationbioconductorbiomartensembl
5.1 match 38 stars 15.99 score 13k scripts 230 dependentsbcgov
bcdata:Search and Retrieve Data from the BC Data Catalogue
Search, query, and download tabular and 'geospatial' data from the British Columbia Data Catalogue (<https://catalogue.data.gov.bc.ca/>). Search catalogue data records based on keywords, data licence, sector, data format, and B.C. government organization. View metadata directly in R, download many data formats, and query 'geospatial' data available via the B.C. government Web Feature Service ('WFS') using 'dplyr' syntax.
Maintained by Andy Teucher. Last updated 1 months ago.
8.0 match 83 stars 10.29 score 186 scripts 4 dependentsncss-tech
aqp:Algorithms for Quantitative Pedology
The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
Maintained by Dylan Beaudette. Last updated 30 days ago.
digital-soil-mappingncss-technrcspedologypedometricssoilsoil-surveyusda
6.9 match 55 stars 11.90 score 1.2k scripts 2 dependentsropensci
rdflib:Tools to Manipulate and Query Semantic Data
The Resource Description Framework, or 'RDF' is a widely used data representation model that forms the cornerstone of the Semantic Web. 'RDF' represents data as a graph rather than the familiar data table or rectangle of relational databases. The 'rdflib' package provides a friendly and concise user interface for performing common tasks on 'RDF' data, such as reading, writing and converting between the various serializations of 'RDF' data, including 'rdfxml', 'turtle', 'nquads', 'ntriples', and 'json-ld'; creating new 'RDF' graphs, and performing graph queries using 'SPARQL'. This package wraps the low level 'redland' R package which provides direct bindings to the 'redland' C library. Additionally, the package supports the newer and more developer friendly 'JSON-LD' format through the 'jsonld' package. The package interface takes inspiration from the Python 'rdflib' library.
Maintained by Carl Boettiger. Last updated 7 months ago.
8.5 match 57 stars 9.59 score 123 scripts 7 dependentsflorianhartig
BayesianTools:General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
General-purpose MCMC and SMC samplers, as well as plots and diagnostic functions for Bayesian statistics, with a particular focus on calibrating complex system models. Implemented samplers include various Metropolis MCMC variants (including adaptive and/or delayed rejection MH), the T-walk, two differential evolution MCMCs, two DREAM MCMCs, and a sequential Monte Carlo (SMC) particle filter.
Maintained by Florian Hartig. Last updated 1 years ago.
bayesecological-modelsmcmcoptimizationsmcsystems-biologycpp
8.0 match 122 stars 10.17 score 580 scripts 5 dependentsstatismike
shiny.reglog:Optional Login and Registration Module System for ShinyApps
RegLog system provides a set of shiny modules to handle register procedure for your users, alongside with login, edit credentials and password reset functionality. It provides support for popular SQL databases and optionally googlesheet-based database for easy setup. For email sending it provides support for 'emayili' and 'gmailr' backends. Architecture makes customizing usability pretty straightforward. The authentication system created with shiny.reglog is designed to be optional: user don't need to be logged-in to access your application, but when logged-in the user data can be used to read from and write to relational databases.
Maintained by Michal Kosinski. Last updated 3 years ago.
googlesheetregister-uishiny-applicationssqlite
12.6 match 14 stars 6.45 score 20 scriptsowp-spatial
hfsubsetR:Hydrofabric Subsetter
Subset Hydrofabric Data in R.
Maintained by Mike Johnson. Last updated 25 days ago.
geospatialhydrofabricnextgennoaa-owpsubsetting
20.1 match 7 stars 4.02 score 8 scriptsduckdb
duckdb:DBI Package for the DuckDB Database Management System
The DuckDB project is an embedded analytical data management system with support for the Structured Query Language (SQL). This package includes all of DuckDB and an R Database Interface (DBI) connector.
Maintained by Kirill Mรผller. Last updated 4 days ago.
5.8 match 158 stars 13.79 score 1.7k scripts 46 dependentscraig-parylo
cvdprevent:Wrapper for the 'CVD Prevent' Application Programming Interface
Provides an R wrapper to the 'CVD Prevent' application programming interface (API). Users can make API requests through built-in R functions. The Cardiovascular Disease Prevention Audit (CVDPREVENT) is an England-wide primary care audit that automatically extracts routinely held GP health data. <https://bmchealthdocs.atlassian.net/wiki/spaces/CP/pages/317882369/CVDPREVENT+API+Documentation>.
Maintained by Craig Parylo. Last updated 1 months ago.
16.0 match 3 stars 5.02 score 4 scriptsepiverse-trace
readepi:Read Data from Health Information Systems
Data import from several health information systems ('HIS'). The current version of the package covers 'HIS' such as 'MS SQL', 'MySQL', and 'PostGRESQL' servers, 'REDCap', 'DHIS2' and 'Fingertips'.
Maintained by Karim Manรฉ. Last updated 9 months ago.
data-importepidemiologyepiversehealth-information-systems
16.6 match 6 stars 4.78 score 5 scriptsbioc
ensembldb:Utilities to create and use Ensembl-based annotation databases
The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.
Maintained by Johannes Rainer. Last updated 5 months ago.
geneticsannotationdatasequencingcoverageannotationbioconductorbioconductor-packagesensembl
5.6 match 35 stars 14.08 score 892 scripts 108 dependentsknausb
vcfR:Manipulate and Visualize VCF Data
Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
Maintained by Brian J. Knaus. Last updated 24 days ago.
genomicspopulation-geneticspopulation-genomicsrcppvcf-datavisualizationzlibcpp
5.8 match 254 stars 13.59 score 3.1k scripts 19 dependentsinlabru-org
inlabru:Bayesian Latent Gaussian Modelling using INLA and Extensions
Facilitates spatial and general latent Gaussian modeling using integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) <doi:10.1111/2041-210X.13168>.
Maintained by Finn Lindgren. Last updated 12 hours ago.
6.3 match 96 stars 12.61 score 832 scripts 6 dependentsdyfanjones
noctua:Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI' Interface)
Designed to be compatible with the 'R' package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws' <https://github.com/paws-r/paws> is used as a driver.
Maintained by Dyfan Jones. Last updated 11 months ago.
10.4 match 46 stars 7.48 score 58 scriptsdavid-cortes
recometrics:Evaluation Metrics for Implicit-Feedback Recommender Systems
Calculates evaluation metrics for implicit-feedback recommender systems that are based on low-rank matrix factorization models, given the fitted model matrices and data, thus allowing to compare models from a variety of libraries. Metrics include P@K (precision-at-k, for top-K recommendations), R@K (recall at k), AP@K (average precision at k), NDCG@K (normalized discounted cumulative gain at k), Hit@K (from which the 'Hit Rate' is calculated), RR@K (reciprocal rank at k, from which the 'MRR' or 'mean reciprocal rank' is calculated), ROC-AUC (area under the receiver-operating characteristic curve), and PR-AUC (area under the precision-recall curve). These are calculated on a per-user basis according to the ranking of items induced by the model, using efficient multi-threaded routines. Also provides functions for creating train-test splits for model fitting and evaluation.
Maintained by David Cortes. Last updated 2 months ago.
implicit-feedbackmatrix-factorizationrecommender-systemsopenblascppopenmp
14.3 match 28 stars 5.45 scorerstudio
reticulate:Interface to 'Python'
Interface to 'Python' modules, classes, and functions. When calling into 'Python', R data types are automatically converted to their equivalent 'Python' types. When values are returned from 'Python' to R they are converted back to R types. Compatible with all versions of 'Python' >= 2.7.
Maintained by Tomasz Kalinowski. Last updated 11 hours ago.
3.7 match 1.7k stars 21.07 score 18k scripts 429 dependentsvoisinneg
queryup:Query the 'UniProtKB' REST API
Retrieve protein information from the 'UniProtKB' REST API (see <https://www.uniprot.org/help/api_queries>).
Maintained by Guillaume Voisinne. Last updated 2 years ago.
18.0 match 4 stars 4.30 score 7 scriptsjulienmoeys
soiltexture:Functions for Soil Texture Plot, Classification and Transformation
"The Soil Texture Wizard" is a set of R functions designed to produce texture triangles (also called texture plots, texture diagrams, texture ternary plots), classify and transform soil textures data. These functions virtually allows to plot any soil texture triangle (classification) into any triangle geometry (isosceles, right-angled triangles, etc.). This set of function is expected to be useful to people using soil textures data from different soil texture classification or different particle size systems. Many (> 15) texture triangles from all around the world are predefined in the package. A simple text based graphical user interface is provided: soiltexture_gui().
Maintained by Julien Moeys. Last updated 1 years ago.
10.8 match 28 stars 7.11 score 136 scripts 1 dependentsbioc
MSstatsQC:Longitudinal system suitability monitoring and quality control for proteomic experiments
MSstatsQC is an R package which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.
Maintained by Eralp Dogu. Last updated 5 months ago.
softwarequalitycontrolproteomicsmassspectrometry
16.9 match 4.48 score 7 scripts 1 dependentsrstudio
shiny:Web Application Framework for R
Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.
Maintained by Winston Chang. Last updated 14 days ago.
reactiverstudioshinyweb-appweb-development
3.5 match 5.4k stars 21.28 score 108k scripts 1.8k dependentsmhahsler
recommenderlab:Lab for Developing and Testing Recommender Algorithms
Provides a research infrastructure to develop and evaluate collaborative filtering recommender algorithms. This includes a sparse representation for user-item matrices, many popular algorithms, top-N recommendations, and cross-validation. Hahsler (2022) <doi:10.48550/arXiv.2205.12371>.
Maintained by Michael Hahsler. Last updated 7 months ago.
collaborative-filteringrecommender-system
7.5 match 214 stars 10.07 score 840 scripts 2 dependentscrunch-io
crunch:Crunch.io Data Tools
The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Maintained by Greg Freedman Ellis. Last updated 12 days ago.
7.2 match 9 stars 10.53 score 200 scripts 2 dependentsnowosad
spDataLarge:Large datasets for spatial analysis
Large datasets for spatial analysis. The data from this package could be retrived using the spData package.
Maintained by Jakub Nowosad. Last updated 5 months ago.
12.3 match 27 stars 6.15 score 1.2k scripts 1 dependentsropensci
webchem:Chemical Information from the Web
Chemical information from around the web. This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.
Maintained by Tamรกs Stirling. Last updated 3 months ago.
cas-numberchemical-informationchemspideridentifierropensciwebscraping
7.3 match 165 stars 10.31 score 173 scripts 10 dependentsbsvars
bsvars:Bayesian Estimation of Structural Vector Autoregressive Models
Provides fast and efficient procedures for Bayesian analysis of Structural Vector Autoregressions. This package estimates a wide range of models, including homo-, heteroskedastic, and non-normal specifications. Structural models can be identified by adjustable exclusion restrictions, time-varying volatility, or non-normality. They all include a flexible three-level equation-specific local-global hierarchical prior distribution for the estimated level of shrinkage for autoregressive and structural parameters. Additionally, the package facilitates predictive and structural analyses such as impulse responses, forecast error variance and historical decompositions, forecasting, verification of heteroskedasticity, non-normality, and hypotheses on autoregressive parameters, as well as analyses of structural shocks, volatilities, and fitted values. Beautiful plots, informative summary functions, and extensive documentation including the vignette by Woลบniak (2024) <doi:10.48550/arXiv.2410.15090> complement all this. The implemented techniques align closely with those presented in Lรผtkepohl, Shang, Uzeda, & Woลบniak (2024) <doi:10.48550/arXiv.2404.11057>, Lรผtkepohl & Woลบniak (2020) <doi:10.1016/j.jedc.2020.103862>, and Song & Woลบniak (2021) <doi:10.1093/acrefore/9780190625979.013.174>. The 'bsvars' package is aligned regarding objects, workflows, and code structure with the R package 'bsvarSIGNs' by Wang & Woลบniak (2024) <doi:10.32614/CRAN.package.bsvarSIGNs>, and they constitute an integrated toolset.
Maintained by Tomasz Woลบniak. Last updated 1 months ago.
bayesian-inferenceeconometricsvector-autoregressionopenblascppopenmp
9.7 match 46 stars 7.67 score 32 scripts 1 dependentsusepa
RAQSAPI:A Simple Interface to the US EPA Air Quality System Data Mart API
Retrieve air monitoring data and associated metadata from the US Environmental Protection Agency's Air Quality System service using functions. See <https://aqs.epa.gov/aqsweb/documents/data_api.html> for details about the US EPA Data Mart API.
Maintained by Clinton Mccrowey. Last updated 9 months ago.
united state environmental protection agencyenvironmental-data-retrievalair-quality-systemaqs-datamartair-monitoringenvironmental-monitoringairmonitoringaqsdatamartr03rprogrammingusepa
11.2 match 21 stars 6.64 score 32 scriptsropensci
comtradr:Interface with the United Nations Comtrade API
Interface with and extract data from the United Nations 'Comtrade' API <https://comtradeplus.un.org/>. 'Comtrade' provides country level shipping data for a variety of commodities, these functions allow for easy API query and data returned as a tidy data frame.
Maintained by Paul Bochtler. Last updated 4 months ago.
apicomtradepeer-reviewedsupply-chain
8.6 match 66 stars 8.67 score 70 scriptsr-simmer
simmer:Discrete-Event Simulation for R
A process-oriented and trajectory-based Discrete-Event Simulation (DES) package for R. It is designed as a generic yet powerful framework. The architecture encloses a robust and fast simulation core written in 'C++' with automatic monitoring capabilities. It provides a rich and flexible R API that revolves around the concept of trajectory, a common path in the simulation model for entities of the same type. Documentation about 'simmer' is provided by several vignettes included in this package, via the paper by Ucar, Smeets & Azcorra (2019, <doi:10.18637/jss.v090.i02>), and the paper by Ucar, Hernรกndez, Serrano & Azcorra (2018, <doi:10.1109/MCOM.2018.1700960>); see 'citation("simmer")' for details.
Maintained by Iรฑaki Ucar. Last updated 6 months ago.
6.5 match 223 stars 11.47 score 440 scripts 6 dependentscamembr
microinverterdata:Collect your Microinverter Data
Collect and normalize local microinverter energy and power production data through off-cloud API requests. Currently supports 'APSystems', 'Enphase', and 'Fronius' microinverters.
Maintained by Christophe Regouby. Last updated 22 days ago.
14.5 match 1 stars 5.08 score 4 scriptsdyfanjones
RAthena:Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Designed to be compatible with the R package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this 'Python' 'Boto3' Software Development Kit ('SDK') <https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Maintained by Dyfan Jones. Last updated 1 years ago.
10.4 match 37 stars 7.10 score 38 scriptszejiang-unsw
synthesis:Generate Synthetic Data from Statistical Models
Generate synthetic time series from commonly used statistical models, including linear, nonlinear and chaotic systems. Applications to testing methods can be found in Jiang, Z., Sharma, A., & Johnson, F. (2019) <doi:10.1016/j.advwatres.2019.103430> and Jiang, Z., Sharma, A., & Johnson, F. (2020) <doi:10.1029/2019WR026962> associated with an open-source tool by Jiang, Z., Rashid, M. M., Johnson, F., & Sharma, A. (2020) <doi:10.1016/j.envsoft.2020.104907>.
Maintained by Ze Jiang. Last updated 9 months ago.
16.2 match 3 stars 4.56 score 12 scriptsropensci
opencage:Geocode with the OpenCage API
Geocode with the OpenCage API, either from place name to longitude and latitude (forward geocoding) or from longitude and latitude to the name and address of a location (reverse geocoding), see <https://opencagedata.com>.
Maintained by Daniel Possenriede. Last updated 2 months ago.
geocodegeocoderopencageopencage-apiopencage-geocoderpeer-reviewedplacenamesrspatial
8.8 match 87 stars 8.39 score 79 scriptsr-lib
gitcreds:Query 'git' Credentials from 'R'
Query, set, delete credentials from the 'git' credential store. Manage 'GitHub' tokens and other 'git' credentials. This package is to be used by other packages that need to authenticate to 'GitHub' and/or other 'git' repositories.
Maintained by Gรกbor Csรกrdi. Last updated 7 months ago.
credentialscredentials-helpergitgithub
5.5 match 28 stars 13.28 score 372 scripts 405 dependentsbioc
AnnotationHub:Client to access AnnotationHub resources
This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
infrastructuredataimportguithirdpartyclientcore-packageu24ca289073
5.3 match 17 stars 13.89 score 2.7k scripts 102 dependentsbioc
regutools:regutools: an R package for data extraction from RegulonDB
RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools provides researchers with the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks.
Maintained by Joselyn Chavez. Last updated 3 months ago.
generegulationgeneexpressionsystemsbiologynetworknetworkinferencevisualizationtranscriptionbioconductorcdsbregulondb
13.8 match 4 stars 5.20 score 6 scriptsrstudio
keras3:R Interface to 'Keras'
Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.
Maintained by Tomasz Kalinowski. Last updated 22 hours ago.
5.3 match 845 stars 13.60 score 264 scripts 2 dependentsjeroen
sys:Powerful and Reliable Tools for Running System Commands in R
Drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. Arguments on Windows automatically get encoded and quoted to work on different locales.
Maintained by Jeroen Ooms. Last updated 6 months ago.
4.9 match 106 stars 14.76 score 191 scripts 5.1k dependentslentinj
mfdb:MareFrame DB Querying Library
Creates and manages a PostgreSQL database suitable for storing fisheries data and aggregating ready for use within a Gadget <https://gadget-framework.github.io/gadget2/> model. See <https://mareframe.github.io/mfdb/> for more information.
Maintained by Jamie Lentin. Last updated 3 years ago.
15.0 match 4.76 score 231 scriptsrstudio
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 12 days ago.
docxeasy-to-usehtmllatexrtfsummary-tables
3.9 match 2.1k stars 18.36 score 20k scripts 112 dependentsarne-henningsen
micEconAids:Demand Analysis with the Almost Ideal Demand System (AIDS)
Functions and tools for analysing consumer demand with the Almost Ideal Demand System (AIDS) suggested by Deaton and Muellbauer (1980).
Maintained by Arne Henningsen. Last updated 3 years ago.
20.9 match 7 stars 3.41 score 37 scriptsmuschellij2
rscopus:Scopus Database 'API' Interface
Uses Elsevier 'Scopus' API <https://dev.elsevier.com/sc_apis.html> to download information about authors and their citations.
Maintained by John Muschelli. Last updated 1 years ago.
7.6 match 77 stars 9.33 score 124 scripts 3 dependentsropensci
sofa:Connector to 'CouchDB'
Provides an interface to the 'NoSQL' database 'CouchDB' (<http://couchdb.apache.org>). Methods are provided for managing databases within 'CouchDB', including creating/deleting/updating/transferring, and managing documents within databases. One can connect with a local 'CouchDB' instance, or a remote 'CouchDB' databases such as 'Cloudant'. Documents can be inserted directly from vectors, lists, data.frames, and 'JSON'. Targeted at 'CouchDB' v2 or greater.
Maintained by Yaoxiang Li. Last updated 1 months ago.
couchdbdatabasenosqldocumentscloudantcouchdb-client
9.3 match 33 stars 7.51 score 54 scriptsohdsi
ResultModelManager:Result Model Manager
Database data model management utilities for R packages in the Observational Health Data Sciences and Informatics program <https://ohdsi.org>. 'ResultModelManager' provides utility functions to allow package maintainers to migrate existing SQL database models, export and import results in consistent patterns.
Maintained by Jamie Gilbert. Last updated 6 months ago.
9.4 match 4 stars 7.38 score 9 scripts 3 dependentshwborchers
pracma:Practical Numerical Math Functions
Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.
Maintained by Hans W. Borchers. Last updated 1 years ago.
5.6 match 29 stars 12.34 score 6.6k scripts 931 dependentshrbrmstr
ggalt:Extra Coordinate Systems, 'Geoms', Statistical Transformations, Scales and Fonts for 'ggplot2'
A compendium of new geometries, coordinate systems, statistical transformations, scales and fonts for 'ggplot2', including splines, 1d and 2d densities, univariate average shifted histograms, a new map coordinate system based on the 'PROJ.4'-library along with geom_cartogram() that mimics the original functionality of geom_map(), formatters for "bytes", a stat_stepribbon() function, increased 'plotly' compatibility and the 'StateFace' open source font 'ProPublica'. Further new functionality includes lollipop charts, dumbbell charts, the ability to encircle points and coordinate-system-based text annotations.
Maintained by Bob Rudis. Last updated 2 years ago.
geomggplot-extensionggplot2ggplot2-geomggplot2-scales
5.5 match 674 stars 12.59 score 2.3k scripts 7 dependentsr-cas
Ryacas:R Interface to the 'Yacas' Computer Algebra System
Interface to the 'yacas' computer algebra system (<http://www.yacas.org/>).
Maintained by Mikkel Meyer Andersen. Last updated 2 years ago.
6.8 match 40 stars 10.15 score 167 scripts 14 dependentsbioc
CuratedAtlasQueryR:Queries the Human Cell Atlas
Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a SingleCellExperiment object.
Maintained by Stefano Mangiola. Last updated 5 months ago.
assaydomaininfrastructurernaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomicsdatabaseduckdbhdf5human-cell-atlassingle-cellsinglecellexperimenttidyverse
9.7 match 90 stars 7.04 score 41 scriptsropensci
rmangal:'Mangal' Client
An interface to the 'Mangal' database - a collection of ecological networks. This package includes functions to work with the 'Mangal RESTful API' methods (<https://mangal-interactions.github.io/mangal-api/>).
Maintained by Kevin Cazelles. Last updated 1 years ago.
ecologynetworksfood websinteractionsdata publicationsopen access
13.5 match 14 stars 5.07 score 28 scriptsnimble-dev
nimble:MCMC, Particle Filtering, and Programmable Hierarchical Modeling
A system for writing hierarchical statistical models largely compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do basic R-style math, and compiling both models and nimbleFunctions via custom-generated C++. 'NIMBLE' includes default methods for MCMC, Laplace Approximation, Monte Carlo Expectation Maximization, and some other tools. The nimbleFunction system makes it easy to do things like implement new MCMC samplers from R, customize the assignment of samplers to different parts of a model from R, and compile the new samplers automatically via C++ alongside the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New distributions and functions can be added, including as calls to external compiled code. Although most people think of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at <https://r-nimble.org>.
Maintained by Christopher Paciorek. Last updated 5 days ago.
bayesian-inferencebayesian-methodshierarchical-modelsmcmcprobabilistic-programmingopenblascpp
5.3 match 169 stars 12.97 score 2.6k scripts 19 dependentsr-forge
mlogit:Multinomial Logit Models
Maximum Likelihood estimation of random utility discrete choice models, as described in Kenneth Train (2009) Discrete Choice Methods with Simulations <doi:10.1017/CBO9780511805271>.
Maintained by Yves Croissant. Last updated 5 years ago.
7.0 match 9.81 score 1.2k scripts 14 dependentstiledb-inc
tiledbcloud:TileDB Cloud Platform R Client Package
The TileDB Cloud Platform API Client Package offers access to the TileDB Cloud service.
Maintained by John Kerl. Last updated 8 months ago.
13.1 match 1 stars 5.22 score 92 scriptsplotly
plotly:Create Interactive Web Graphics via 'plotly.js'
Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Maintained by Carson Sievert. Last updated 3 months ago.
d3jsdata-visualizationggplot2javascriptplotlyshinywebgl
3.5 match 2.6k stars 19.43 score 93k scripts 797 dependentsr-spatial
rgee:R Bindings for Calling the 'Earth Engine' API
Earth Engine <https://earthengine.google.com/> client library for R. All of the 'Earth Engine' API classes, modules, and functions are made available. Additional functions implemented include importing (exporting) of Earth Engine spatial objects, extraction of time series, interactive map display, assets management interface, and metadata display. See <https://r-spatial.github.io/rgee/> for further details.
Maintained by Cesar Aybar. Last updated 5 days ago.
earth-engineearthenginegoogle-earth-enginegoogleearthenginespatial-analysisspatial-data
4.9 match 715 stars 13.77 score 1.9k scripts 3 dependentsbioc
multiMiR:Integration of multiple microRNA-target databases with their disease and drug associations
A collection of microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).
Maintained by Spencer Mahaffey. Last updated 5 months ago.
mirnadatahomo_sapiens_datamus_musculus_datarattus_norvegicus_dataorganismdatamicrorna-sequencesql
8.0 match 20 stars 8.45 score 141 scripts