Showing 200 of total 1070 results (show query)
proteomicslab57357
UniprotR:Retrieving Information of Proteins from Uniprot
Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <https://www.sciencedirect.com/science/article/pii/S1874391919303859>.
Maintained by Mohamed Soudy. Last updated 2 years ago.
103.7 match 61 stars 7.65 score 89 scripts 1 dependents
rstudio
connections:Integrates with the 'RStudio' Connections Pane and 'pins'
Enables 'DBI' compliant packages to integrate with the 'RStudio' connections pane, and the 'pins' package. It automates the display of schemata, tables, views, as well as the preview of the table's top 1000 records.
Maintained by Edgar Ruiz. Last updated 1 years ago.
connection-panedatabase-connectionpinsrstudio
82.5 match 57 stars 6.50 score 124 scripts 1 dependents
igraph
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 Müller. Last updated 9 hours ago.
complex-networksgraph-algorithmsgraph-theorymathematicsnetwork-analysisnetwork-graphfortranlibxml2glpkopenblascpp
22.6 match 582 stars 21.11 score 31k scripts 1.9k dependents
ohdsi
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 1 months ago.
34.8 match 56 stars 12.63 score 772 scripts 11 dependents
posit-dev
connectapi:Utilities for Interacting with the 'Posit Connect' Server API
Provides a helpful 'R6' class and methods for interacting with the 'Posit Connect' Server API along with some meaningful utility functions for regular tasks. API documentation varies by 'Posit Connect' installation and version, but the latest documentation is also hosted publicly at <https://docs.posit.co/connect/api/>.
Maintained by Toph Allen. Last updated 3 days ago.
37.9 match 47 stars 10.48 score 252 scripts 1 dependents
r-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 Müller. Last updated 3 months ago.
18.8 match 302 stars 20.88 score 19k scripts 2.9k dependents
spatstat
spatstat.geom:Geometrical Functionality of the 'spatstat' Family
Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)
Maintained by Adrian Baddeley. Last updated 2 days ago.
classes-and-objectsdistance-calculationgeometrygeometry-processingimagesmensurationplottingpoint-patternsspatial-dataspatial-data-analysis
31.4 match 7 stars 12.11 score 241 scripts 227 dependentsr-dbi
odbc:Connect to ODBC Compatible Databases (using the DBI Interface)
A DBI-compatible interface to ODBC databases.
Maintained by Hadley Wickham. Last updated 13 days ago.
21.2 match 396 stars 16.22 score 2.9k scripts 22 dependents
american-institutes-for-research
EdSurvey:Analysis of NCES Education Survey and Assessment Data
Read in and analyze functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: Organisation for Economic Co-operation and Development (OECD) <https://www.oecd.org/en/about/directorates/directorate-for-education-and-skills.html>, including Programme for International Student Assessment (PISA), Teaching and Learning International Survey (TALIS), Programme for the International Assessment of Adult Competencies (PIAAC), and International Association for the Evaluation of Educational Achievement (IEA) <https://www.iea.nl/>, including Trends in International Mathematics and Science Study (TIMSS), TIMSS Advanced, Progress in International Reading Literacy Study (PIRLS), International Civic and Citizenship Study (ICCS), International Computer and Information Literacy Study (ICILS), and Civic Education Study (CivEd).
Maintained by Paul Bailey. Last updated 16 days ago.
39.7 match 10 stars 7.86 score 139 scripts 1 dependents
rich-iannone
DiagrammeR:Graph/Network Visualization
Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.
Maintained by Richard Iannone. Last updated 2 months ago.
graphgraph-functionsnetwork-graphproperty-graphvisualization
18.1 match 1.7k stars 15.18 score 3.8k scripts 87 dependents
bioc
GRaNIE:GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data
Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have cell-type specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (GRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a GRN using single-cell or bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally (Capture) Hi-C data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach.
Maintained by Christian Arnold. Last updated 5 months ago.
softwaregeneexpressiongeneregulationnetworkinferencegenesetenrichmentbiomedicalinformaticsgeneticstranscriptomicsatacseqrnaseqgraphandnetworkregressiontranscriptionchipseq
48.9 match 5.40 score 24 scripts
paws-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 3 days ago.
22.6 match 332 stars 11.25 score 177 scripts 12 dependents
henrikbengtsson
R.utils:Various Programming Utilities
Utility functions useful when programming and developing R packages.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
18.2 match 63 stars 13.74 score 5.7k scripts 814 dependents
sparklyr
sparklyr:R Interface to Apache Spark
R interface to Apache Spark, a fast and general engine for big data processing, see <https://spark.apache.org/>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.
Maintained by Edgar Ruiz. Last updated 10 days ago.
apache-sparkdistributeddplyridelivymachine-learningremote-clusterssparksparklyr
15.2 match 959 stars 15.16 score 4.0k scripts 21 dependents
achubaty
grainscape:Landscape Connectivity, Habitat, and Protected Area Networks
Given a landscape resistance surface, creates minimum planar graph (Fall et al. (2007) <doi:10.1007/s10021-007-9038-7>) and grains of connectivity (Galpern et al. (2012) <doi:10.1111/j.1365-294X.2012.05677.x>) models that can be used to calculate effective distances for landscape connectivity at multiple scales. Documentation is provided by several vignettes, and a paper (Chubaty, Galpern & Doctolero (2020) <doi:10.1111/2041-210X.13350>).
Maintained by Alex M Chubaty. Last updated 2 months ago.
habitat-connectivitylandscape-connectivityspatial-graphscpp
33.8 match 20 stars 6.78 score 20 scripts
kwstat
connected:Visualize and Improve Connectedness of Factors in Tables
Visualize the connectedness of factors in two-way tables. Perform two-way filtering to improve the degree of connectedness. See Weeks & Williams (1964) <doi:10.1080/00401706.1964.10490188>.
Maintained by Kevin Wright. Last updated 13 days ago.
53.3 match 4.18 score
jiefei-wang
aws.ecx:Communicating with AWS EC2 and ECS using AWS REST APIs
Providing the functions for communicating with Amazon Web Services(AWS) Elastic Compute Cloud(EC2) and Elastic Container Service(ECS). The functions will have the prefix 'ecs_' or 'ec2_' depending on the class of the API. The request will be sent via the REST API and the parameters are given by the function argument. The credentials can be set via 'aws_set_credentials'. The EC2 documentation can be found at <https://docs.aws.amazon.com/AWSEC2/latest/APIReference/Welcome.html> and ECS can be found at <https://docs.aws.amazon.com/AmazonECS/latest/APIReference/Welcome.html>.
Maintained by Jiefei Wang. Last updated 3 years ago.
52.4 match 1 stars 4.18 score 2 scripts
josherrickson
rlemon:R Access to LEMON Graph Algorithms
Allows easy access to the LEMON Graph Library set of algorithms, written in C++. See the LEMON project page at <https://lemon.cs.elte.hu/trac/lemon>. Current LEMON version is 1.3.1.
Maintained by Josh Errickson. Last updated 2 months ago.
29.2 match 8 stars 7.04 score 1 scripts 13 dependents
prioritizr
prioritizr:Systematic Conservation Prioritization in R
Systematic conservation prioritization using mixed integer linear programming (MILP). It provides a flexible interface for building and solving conservation planning problems. Once built, conservation planning problems can be solved using a variety of commercial and open-source exact algorithm solvers. By using exact algorithm solvers, solutions can be generated that are guaranteed to be optimal (or within a pre-specified optimality gap). Furthermore, conservation problems can be constructed to optimize the spatial allocation of different management actions or zones, meaning that conservation practitioners can identify solutions that benefit multiple stakeholders. To solve large-scale or complex conservation planning problems, users should install the Gurobi optimization software (available from <https://www.gurobi.com/>) and the 'gurobi' R package (see Gurobi Installation Guide vignette for details). Users can also install the IBM CPLEX software (<https://www.ibm.com/products/ilog-cplex-optimization-studio/cplex-optimizer>) and the 'cplexAPI' R package (available at <https://github.com/cran/cplexAPI>). Additionally, the 'rcbc' R package (available at <https://github.com/dirkschumacher/rcbc>) can be used to generate solutions using the CBC optimization software (<https://github.com/coin-or/Cbc>). For further details, see Hanson et al. (2025) <doi:10.1111/cobi.14376>.
Maintained by Richard Schuster. Last updated 11 days ago.
biodiversityconservationconservation-planneroptimizationprioritizationsolverspatialcpp
17.0 match 124 stars 11.82 score 584 scripts 2 dependents
majerr
sqlhelper:Easier 'SQL' Integration
Execute files of 'SQL' and manage database connections. 'SQL' statements and queries may be interpolated with string literals. Execution of individual statements and queries may be controlled with keywords. Multiple connections may be defined with 'YAML' and accessed by name.
Maintained by Matthew Roberts. Last updated 1 years ago.
36.2 match 2 stars 5.19 score 39 scripts
darwin-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 18 days ago.
16.5 match 12 stars 11.39 score 502 scripts 12 dependents
r-lib
archive:Multi-Format Archive and Compression Support
Bindings to 'libarchive' <http://www.libarchive.org> the Multi-format archive and compression library. Offers R connections and direct extraction for many archive formats including 'tar', 'ZIP', '7-zip', 'RAR', 'CAB' and compression formats including 'gzip', 'bzip2', 'compress', 'lzma' and 'xz'.
Maintained by Gábor Csárdi. Last updated 1 months ago.
compressionconnectionslibarchivecpp
15.9 match 145 stars 11.77 score 494 scripts 27 dependents
tgrimes
SeqNet:Generate RNA-Seq Data from Gene-Gene Association Networks
Methods to generate random gene-gene association networks and simulate RNA-seq data from them, as described in Grimes and Datta (2021) <doi:10.18637/jss.v098.i12>. Includes functions to generate random networks of any size and perturb them to obtain differential networks. Network objects are built from individual, overlapping modules that represent pathways. The resulting network has various topological properties that are characteristic of gene regulatory networks. RNA-seq data can be generated such that the association among gene expression profiles reflect the underlying network. A reference RNA-seq dataset can be provided to model realistic marginal distributions. Plotting functions are available to visualize a network, compare two networks, and compare the expression of two genes across multiple networks.
Maintained by Tyler Grimes. Last updated 4 years ago.
58.5 match 2.82 score 22 scripts 1 dependents
pecanproject
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 2 days ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants
13.3 match 216 stars 11.88 score 127 scripts 27 dependentsspatstat
spatstat.linnet:Linear Networks Functionality of the 'spatstat' Family
Defines types of spatial data on a linear network and provides functionality for geometrical operations, data analysis and modelling of data on a linear network, in the 'spatstat' family of packages. Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks. Data types defined on a network include point patterns, pixel images, functions, and tessellations. Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported. Parametric models can be fitted to point pattern data using the function lppm() similar to glm(). Only Poisson models are implemented so far. Models may involve dependence on covariates and dependence on marks. Models are fitted by maximum likelihood. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots. Random point patterns on a network can be generated using a variety of models.
Maintained by Adrian Baddeley. Last updated 2 months ago.
density-estimationheat-equationkernel-density-estimationnetwork-analysispoint-processesspatial-data-analysisstatistical-analysisstatistical-inferencestatistical-models
16.1 match 6 stars 9.64 score 35 scripts 43 dependents
nikolaus77
rocker:Database Interface Class
'R6' class interface for handling relational database connections using 'DBI' package as backend. The class allows handling of connections to e.g. PostgreSQL, MariaDB and SQLite. The purpose is having an intuitive object allowing straightforward handling of SQL databases.
Maintained by Nikolaus Pawlowski. Last updated 3 years ago.
databasedbimariadbmysqlpostgrespostgresqlr6sqlsqlite
28.1 match 5 stars 5.24 score 7 scripts
apache
arrow:Integration to 'Apache' 'Arrow'
'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an interface to the 'Arrow C++' library.
Maintained by Jonathan Keane. Last updated 1 months ago.
7.4 match 15k stars 19.22 score 10k scripts 81 dependents
vubiostat
redcapAPI:Interface to 'REDCap'
Access data stored in 'REDCap' databases using the Application Programming Interface (API). 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>, Harris, et al. (2009) <doi:10.1016/j.jbi.2008.08.010>, Harris, et al. (2019) <doi:10.1016/j.jbi.2019.103208>) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The API allows users to access data and project meta data (such as the data dictionary) from the web programmatically. The 'redcapAPI' package facilitates the process of accessing data with options to prepare an analysis-ready data set consistent with the definitions in a database's data dictionary.
Maintained by Shawn Garbett. Last updated 9 days ago.
13.5 match 22 stars 10.47 score 134 scripts 2 dependents
open-eo
openeo:Client Interface for 'openEO' Servers
Access data and processing functionalities of 'openEO' compliant back-ends in R.
Maintained by Florian Lahn. Last updated 2 months ago.
16.0 match 64 stars 8.65 score 128 scriptspaws-r
paws.customer.engagement:'Amazon Web Services' Customer Engagement Services
Interface to 'Amazon Web Services' customer engagement services, including 'Simple Email Service', 'Connect' contact center service, and more <https://aws.amazon.com/>.
Maintained by Dyfan Jones. Last updated 3 days ago.
15.3 match 332 stars 9.01 score 13 dependentsrstudio
rscontract:Generic implementation of the 'RStudio' connections contract
Provides a generic implementation of the 'RStudio' connection contract to make it easier for database connections, and other type of connections, opened via R packages integrate with the connections pane inside the 'RStudio' interactive development environment (IDE).
Maintained by Nathan Stephens. Last updated 4 years ago.
25.5 match 22 stars 5.12 score 4 scripts 2 dependents
ropensci
nodbi:'NoSQL' Database Connector
Simplified JSON document database access and manipulation, providing a common API across supported 'NoSQL' databases 'Elasticsearch', 'CouchDB', 'MongoDB' as well as 'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Maintained by Ralf Herold. Last updated 4 months ago.
databasemongodbelasticsearchcouchdbsqlitepostgresqlduckdbnosqljsondocuments
15.4 match 78 stars 8.36 score 28 scripts 1 dependents
coolbutuseless
ctypesio:Read and Write Standard 'C' Types from Files, Connections and Raw Vectors
Interacting with binary files can be difficult because R's types are a subset of what is generally supported by 'C'. This package provides a suite of functions for reading and writing binary data (with files, connections, and raw vectors) using 'C' type descriptions. These functions convert data between 'C' types and R types while checking for values outside the type limits, 'NA' values, etc.
Maintained by Mike Cheng. Last updated 2 months ago.
21.1 match 5 stars 6.02 score 6 scripts 1 dependents
plangfelder
WGCNA:Weighted Correlation Network Analysis
Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Maintained by Peter Langfelder. Last updated 6 months ago.
12.5 match 54 stars 9.65 score 5.3k scripts 32 dependentsapache
adbcdrivermanager:'Arrow' Database Connectivity ('ADBC') Driver Manager
Provides a developer-facing interface to 'Arrow' Database Connectivity ('ADBC') for the purposes of driver development, driver testing, and building high-level database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters.
Maintained by Dewey Dunnington. Last updated 2 days ago.
10.5 match 417 stars 11.44 score 73 scripts 6 dependents
jumpingrivers
audit.connect:Posit Connect Health Check
Posit Connect Health Check. Deploys various content types to assess whether Connect is functioning correctly.
Maintained by Jumping Rivers. Last updated 1 months ago.
43.4 match 2.70 score 1 scripts
dmkaplan2000
ConnMatTools:Tools for Working with Connectivity Data
Collects several different methods for analyzing and working with connectivity data in R. Though primarily oriented towards marine larval dispersal, many of the methods are general and useful for terrestrial systems as well.
Maintained by David M. Kaplan. Last updated 5 years ago.
33.4 match 3.48 score 60 scripts
zachcp
rcdk:Interface to the 'CDK' Libraries
Allows the user to access functionality in the 'CDK', a Java framework for chemoinformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on. In addition, the 'CDK' API allows the user to view structures in 2D.
Maintained by Zachary Charlop-Powers. Last updated 2 years ago.
16.5 match 1 stars 6.78 score 287 scripts 11 dependentsrstudio
pins:Pin, Discover, and Share Resources
Publish data sets, models, and other R objects, making it easy to share them across projects and with your colleagues. You can pin objects to a variety of "boards", including local folders (to share on a networked drive or with 'DropBox'), 'Posit Connect', 'AWS S3', and more.
Maintained by Julia Silge. Last updated 1 months ago.
azuregcloudrpinsrsconnects3storage
7.9 match 321 stars 14.17 score 1.9k scripts 17 dependents
nflverse
nflreadr:Download 'nflverse' Data
A minimal package for downloading data from 'GitHub' repositories of the 'nflverse' project.
Maintained by Tan Ho. Last updated 4 months ago.
nflnflfastrnflversesports-data
8.9 match 66 stars 12.46 score 476 scripts 10 dependents
schw4b
DGM:Dynamic Graphical Models
Dynamic graphical models for multivariate time series data to estimate directed dynamic networks in functional magnetic resonance imaging (fMRI), see Schwab et al. (2017) <doi:10.1016/j.neuroimage.2018.03.074>.
Maintained by Simon Schwab. Last updated 3 years ago.
dynamic-graphical-modelsfunctional-connectivitytime-varying-connectivityopenblascppopenmp
19.2 match 25 stars 5.49 score 25 scriptsbioc
martini:GWAS Incorporating Networks
martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork.
Maintained by Hector Climente-Gonzalez. Last updated 5 months ago.
softwaregenomewideassociationsnpgeneticvariabilitygeneticsfeatureextractiongraphandnetworknetworkbioinformaticsgenomicsgwasnetwork-analysissnpssystems-biologycpp
16.9 match 4 stars 6.16 score 30 scripts
t-kalinowski
keras: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 11 months ago.
9.5 match 10.82 score 10k scripts 54 dependents
winvector
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.
10.8 match 110 stars 9.53 score 126 scripts 3 dependents
thinkr-open
gitlabr:Access to the 'GitLab' API
Provides R functions to access the API of the project and repository management web application 'GitLab'. For many common tasks (repository file access, issue assignment and status, commenting) convenience wrappers are provided, and in addition the full API can be used by specifying request locations. 'GitLab' is open-source software and can be self-hosted or used on <https://about.gitlab.com>.
Maintained by Sébastien Rochette. Last updated 10 months ago.
12.1 match 40 stars 8.40 score 69 scripts 1 dependentsbioc
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 2 days ago.
annotationbioconductorbiomartensembl
6.3 match 38 stars 15.99 score 13k scripts 230 dependents
inbo
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 25 days ago.
16.5 match 6.16 score 114 scripts 1 dependents
cran
RODBC:ODBC Database Access
An ODBC database interface.
Maintained by Brian Ripley. Last updated 3 months ago.
13.5 match 10 stars 7.41 score 38 dependents
tomasfryda
h2o:R Interface for the 'H2O' Scalable Machine Learning Platform
R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection, Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).
Maintained by Tomas Fryda. Last updated 1 years ago.
11.7 match 3 stars 8.20 score 7.8k scripts 11 dependents
thomasp85
ggraph:An Implementation of Grammar of Graphics for Graphs and Networks
The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.
Maintained by Thomas Lin Pedersen. Last updated 1 years ago.
ggplot-extensionggplot2graph-visualizationnetwork-visualizationvisualizationcpp
5.6 match 1.1k stars 16.96 score 9.2k scripts 111 dependents
frbcesab
chessboard:Create Network Connections Based on Chess Moves
Provides functions to work with directed (asymmetric) and undirected (symmetric) spatial networks. It makes the creation of connectivity matrices easier, i.e. a binary matrix of dimension n x n, where n is the number of nodes (sampling units) indicating the presence (1) or the absence (0) of an edge (link) between pairs of nodes. Different network objects can be produced by 'chessboard': node list, neighbor list, edge list, connectivity matrix. It can also produce objects that will be used later in Moran's Eigenvector Maps (Dray et al. (2006) <doi:10.1016/j.ecolmodel.2006.02.015>) and Asymetric Eigenvector Maps (Blanchet et al. (2008) <doi:10.1016/j.ecolmodel.2008.04.001>), methods available in the package 'adespatial' (Dray et al. (2023) <https://CRAN.R-project.org/package=adespatial>). This work is part of the FRB-CESAB working group Bridge <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/bridge/>.
Maintained by Nicolas Casajus. Last updated 1 years ago.
connectivity-matrixdirected-networksneighborhoodnetworkone-dimensional-networksspatial-networkstwo-dimensional-networksundirected-networks
20.0 match 4 stars 4.78 scorebioc
PharmacoGx:Analysis of Large-Scale Pharmacogenomic Data
Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.
Maintained by Benjamin Haibe-Kains. Last updated 2 months ago.
geneexpressionpharmacogeneticspharmacogenomicssoftwareclassificationdatasetspharmacogenomicpharmacogxcpp
8.3 match 68 stars 11.39 score 442 scripts 3 dependentsrstudio
connectwidgets:Organize and Curate Your Content Within 'Posit Connect'
A collection of helper functions and 'htmlwidgets' to help publishers curate content collections on 'Posit Connect'. The components, Card, Grid, Table, Search, and Filter can be used to produce a showcase page or gallery contained within a static or interactive R Markdown page.
Maintained by Brian Smith. Last updated 6 months ago.
13.7 match 22 stars 6.80 score 36 scripts
smbc-nzp
MigConnectivity:Estimate Migratory Connectivity for Migratory Animals
Allows the user to estimate transition probabilities for migratory animals between any two phases of the annual cycle, using a variety of different data types. Also quantifies the strength of migratory connectivity (MC), a standardized metric to quantify the extent to which populations co-occur between two phases of the annual cycle. Includes functions to estimate MC and the more traditional metric of migratory connectivity strength (Mantel correlation) incorporating uncertainty from multiple sources of sampling error. For cross-species comparisons, methods are provided to estimate differences in migratory connectivity strength, incorporating uncertainty. See Cohen et al. (2018) <doi:10.1111/2041-210X.12916>, Cohen et al. (2019) <doi:10.1111/ecog.03974>, and Roberts et al. (2023) <doi:10.1002/eap.2788> for details on some of these methods.
Maintained by Jeffrey A. Hostetler. Last updated 12 months ago.
13.6 match 8 stars 6.77 score 41 scripts
fmestre1
lconnect:Simple Tools to Compute Landscape Connectivity Metrics
Provides functions to upload vectorial data and derive landscape connectivity metrics in habitat or matrix systems. Additionally, includes an approach to assess individual patch contribution to the overall landscape connectivity, enabling the prioritization of habitat patches. The computation of landscape connectivity and patch importance are very useful in Landscape Ecology research. The metrics available are: number of components, number of links, size of the largest component, mean size of components, class coincidence probability, landscape coincidence probability, characteristic path length, expected cluster size, area-weighted flux and integral index of connectivity. Pascual-Hortal, L., and Saura, S. (2006) <doi:10.1007/s10980-006-0013-z> Urban, D., and Keitt, T. (2001) <doi:10.2307/2679983> Laita, A., Kotiaho, J., Monkkonen, M. (2011) <doi:10.1007/s10980-011-9620-4>.
Maintained by Frederico Mestre. Last updated 1 years ago.
connectivityhabitat-connectivitylandscapemetricscpp
23.4 match 6 stars 3.78 score 3 scripts
ffverse
ffscrapr:API Client for Fantasy Football League Platforms
Helps access various Fantasy Football APIs by handling authentication and rate-limiting, forming appropriate calls, and returning tidy dataframes which can be easily connected to other data sources.
Maintained by Tan Ho. Last updated 5 months ago.
api-clientfantasy-footballfantasy-football-api
10.8 match 84 stars 8.07 score 178 scripts 1 dependents
cwatson
brainGraph:Graph Theory Analysis of Brain MRI Data
A set of tools for performing graph theory analysis of brain MRI data. It works with data from a Freesurfer analysis (cortical thickness, volumes, local gyrification index, surface area), diffusion tensor tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from DPABI). It contains a graphical user interface for graph visualization and data exploration, along with several functions for generating useful figures.
Maintained by Christopher G. Watson. Last updated 1 years ago.
brain-connectivitybrain-imagingcomplex-networksconnectomeconnectomicsfmrigraph-theorymrinetwork-analysisneuroimagingneurosciencestatisticstractography
11.1 match 188 stars 7.86 score 107 scripts 3 dependentsbioc
RCy3:Functions to Access and Control Cytoscape
Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.
Maintained by Alex Pico. Last updated 5 months ago.
visualizationgraphandnetworkthirdpartyclientnetwork
6.3 match 52 stars 13.39 score 628 scripts 15 dependents
hsonne
odbc32:32-bit ODBC drivers for 64-bit R sessions
Tools for using 32-bit ODBC drivers from 64-bit R sessions. Based on socket connection between 64-bit R and host 32-bit R.
Maintained by Vaclav Hausenblas. Last updated 5 years ago.
23.4 match 3.54 score 6 scripts 23 dependentsrstudio
rsconnect:Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io', and 'RPubs'
Programmatic deployment interface for 'RPubs', 'shinyapps.io', and 'Posit Connect'. Supported content types include R Markdown documents, Shiny applications, Plumber APIs, plots, and static web content.
Maintained by Aron Atkins. Last updated 16 days ago.
5.2 match 139 stars 14.90 score 3.1k scripts 6 dependents
yunuuuu
ggalign:A 'ggplot2' Extension for Consistent Axis Alignment
A 'ggplot2' extension offers various tools the creation of complex, multi-plot visualizations. Built on the familiar grammar of graphics, it provides intuitive tools to align and organize plots, making it ideal for complex visualizations. It excels in multi-omics research—such as genomics and microbiomes—by simplifying the visualization of intricate relationships between datasets, for example, linking genes to pathways. Whether you need to stack plots, arrange them around a central figure, or create a circular layout, 'ggalign' delivers flexibility and accuracy with minimal effort.
Maintained by Yun Peng. Last updated 17 hours ago.
complex-heatmapsdendrogramdendrogram-heatmapggplotggplot-extensionggplot2heatmapheatmap-visualizationheatmapsmarginal-plotsoncoplotoncoprinttanglegramupsetupsetplot
10.9 match 267 stars 7.08 score 27 scriptsffverse
ffsimulator:Simulate Fantasy Football Seasons
Uses bootstrap resampling to run fantasy football season simulations supported by historical rankings and 'nflfastR' data, calculating optimal lineups, and returning aggregated results.
Maintained by Tan Ho. Last updated 5 months ago.
14.8 match 17 stars 5.17 score 44 scripts
jeroen
curl:A Modern and Flexible Web Client for R
Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.
Maintained by Jeroen Ooms. Last updated 22 days ago.
3.8 match 224 stars 19.98 score 4.0k scripts 5.9k dependents
asgr
imager:Image Processing Library Based on 'CImg'
Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.
Maintained by Aaron Robotham. Last updated 27 days ago.
5.6 match 17 stars 13.62 score 2.4k scripts 45 dependentsbioc
RBGL:An interface to the BOOST graph library
A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.
Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.
8.9 match 8.59 score 320 scripts 132 dependents
thewileylab
ReviewR:A Light-Weight, Portable Tool for Reviewing Individual Patient Records
A portable Shiny tool to explore patient-level electronic health record data and perform chart review in a single integrated framework. This tool supports browsing clinical data in many different formats including multiple versions of the 'OMOP' common data model as well as the 'MIMIC-III' data model. In addition, chart review information is captured and stored securely via the Shiny interface in a 'REDCap' (Research Electronic Data Capture) project using the 'REDCap' API. See the 'ReviewR' website for additional information, documentation, and examples.
Maintained by David Mayer. Last updated 2 years ago.
12.0 match 24 stars 6.33 score 6 scriptsr-lib
withr:Run Code 'With' Temporarily Modified Global State
A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.
Maintained by Lionel Henry. Last updated 19 days ago.
4.3 match 176 stars 17.92 score 1.2k scripts 12k dependents
dyfanjones
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.
10.5 match 37 stars 7.10 score 38 scriptsropensci
RSelenium:R Bindings for 'Selenium WebDriver'
Provides a set of R bindings for the 'Selenium 2.0 WebDriver' (see <https://www.selenium.dev/documentation/> for more information) using the 'JsonWireProtocol' (see <https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol> for more information). 'Selenium 2.0 WebDriver' allows driving a web browser natively as a user would either locally or on a remote machine using the Selenium server it marks a leap forward in terms of web browser automation. Selenium automates web browsers (commonly referred to as browsers). Using RSelenium you can automate browsers locally or remotely.
Maintained by Jonathan Völkle. Last updated 2 years ago.
5.5 match 344 stars 13.38 score 1.9k scripts 12 dependents
cedricbriandgithub
stacomiR:Fish Migration Monitoring
Graphical outputs and treatment for a database of fish pass monitoring. It is a part of the 'STACOMI' open source project developed in France by the French Office for Biodiversity institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See <http://stacomir.r-forge.r-project.org/> for more information on 'STACOMI'.
Maintained by Cedric Briand. Last updated 1 years ago.
29.4 match 1 stars 2.43 score 27 scripts
mbtyers
riverdist:River Network Distance Computation and Applications
Reads river network shape files and computes network distances. Also included are a variety of computation and graphical tools designed for fisheries telemetry research, such as minimum home range, kernel density estimation, and clustering analysis using empirical k-functions with a bootstrap envelope. Tools are also provided for editing the river networks, meaning there is no reliance on external software.
Maintained by Matt Tyers. Last updated 4 months ago.
9.4 match 26 stars 7.50 score 96 scripts
jokergoo
circlize:Circular Visualization
Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data. The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.
Maintained by Zuguang Gu. Last updated 1 years ago.
4.5 match 983 stars 15.62 score 10k scripts 213 dependentsropensci
restez:Create and Query a Local Copy of 'GenBank' in R
Download large sections of 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local SQL-based database. A user can then query this database using 'restez' functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez> wrappers.
Maintained by Joel H. Nitta. Last updated 10 days ago.
9.9 match 26 stars 7.01 score 175 scripts 1 dependents
kwb-r
kwb.db:Functions supporting data base access
This package contains some useful functions, especially for simplifying data transfer between MS Access databases and R. With the functions of this package it is not needed any more to open and close a database connection explicitely; this is done 'behind the scenes' in the functions. Instead of a database connection the path to the database file needs to be passed to the functions as an argument. The main functions are hsGetTable and hsPutTable which transfer data from an MS Access database to a data frame in R and save data from a data frame in R into a table in an MS Access database, respectively. Take care when getting time series data from an MS Access database, see therefore hsMdbTimeSeries. Use hsTables to get a list of tables that are available in a database and hsFields to get a list of table fields that are contained in a database table.
Maintained by Hauke Sonnenberg. Last updated 1 years ago.
data-importdatabase-accessdatabase-connectionrodbc
19.8 match 3.52 score 5 scripts 22 dependents
ssi-dk
SCDB:Easily Access and Maintain Time-Based Versioned Data (Slowly-Changing-Dimension)
A collection of functions that enable easy access and updating of a database of data over time. More specifically, the package facilitates type-2 history for data-warehouses and provides a number of Quality of life improvements for working on SQL databases with R. For reference see Ralph Kimball and Margy Ross (2013, ISBN 9781118530801).
Maintained by Rasmus Skytte Randløv. Last updated 17 days ago.
9.4 match 6 stars 7.38 score 11 scripts 1 dependents
natverse
nat:NeuroAnatomy Toolbox for Analysis of 3D Image Data
NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Maintained by Gregory Jefferis. Last updated 5 months ago.
3dconnectomicsimage-analysisneuroanatomyneuroanatomy-toolboxneuronneuron-morphologyneurosciencevisualisation
6.9 match 67 stars 9.94 score 436 scripts 2 dependents
cjvanlissa
worcs:Workflow for Open Reproducible Code in Science
Create reproducible and transparent research projects in 'R'. This package is based on the Workflow for Open Reproducible Code in Science (WORCS), a step-by-step procedure based on best practices for Open Science. It includes an 'RStudio' project template, several convenience functions, and all dependencies required to make your project reproducible and transparent. WORCS is explained in the tutorial paper by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021). <doi:10.3233/DS-210031>.
Maintained by Caspar J. Van Lissa. Last updated 11 days ago.
7.4 match 83 stars 9.26 score 59 scripts
spatialnous
alcyon:Spatial Network Analysis
Interface package for 'sala', the spatial network analysis library from the 'depthmapX' software application. The R parts of the code are based on the 'rdepthmap' package. Allows for the analysis of urban and building-scale networks and provides metrics and methods usually found within the Space Syntax domain. Methods in this package are described by K. Al-Sayed, A. Turner, B. Hillier, S. Iida and A. Penn (2014) "Space Syntax methodology", and also by A. Turner (2004) <https://discovery.ucl.ac.uk/id/eprint/2651> "Depthmap 4: a researcher's handbook".
Maintained by Petros Koutsolampros. Last updated 2 months ago.
10.8 match 2 stars 6.34 score 13 scripts
uofuepibio
epiworldR:Fast Agent-Based Epi Models
A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Maintained by Andrew Pulsipher. Last updated 11 days ago.
abmagent-based-modelingcovid-19epidemicsepidemiologyr-programmingrpackrpkgseirseir-modelsimulationsirsir-modelcppopenmp
8.1 match 9 stars 8.33 score 58 scripts 1 dependents
damianobaldan
riverconn:Fragmentation and Connectivity Indices for Riverscapes
Indices for assessing riverscape fragmentation, including the Dendritic Connectivity Index, the Population Connectivity Index, the River Fragmentation Index, the Probability of Connectivity, and the Integral Index of connectivity. For a review, see Jumani et al. (2020) <doi:10.1088/1748-9326/abcb37> and Baldan et al. (2022) <doi:10.1016/j.envsoft.2022.105470> Functions to calculate temporal indices improvement when fragmentation due to barriers is reduced are also included.
Maintained by Damiano Baldan. Last updated 12 months ago.
14.1 match 9 stars 4.77 score 13 scriptsdyfanjones
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.
8.7 match 46 stars 7.48 score 58 scriptsropensci
opentripplanner:Setup and connect to 'OpenTripPlanner'
Setup and connect to 'OpenTripPlanner' (OTP) <http://www.opentripplanner.org/>. OTP is an open source platform for multi-modal and multi-agency journey planning written in 'Java'. The package allows you to manage a local version or connect to remote OTP server to find walking, cycling, driving, or transit routes. This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).
Maintained by Malcolm Morgan. Last updated 3 months ago.
dataisochronesjavaopentripplannerotppublic-transportroutingtransporttransportation-planning
7.3 match 83 stars 8.94 score 147 scriptsrstudio
pool:Object Pooling
Enables the creation of object pools, which make it less computationally expensive to fetch a new object. Currently the only supported pooled objects are 'DBI' connections.
Maintained by Hadley Wickham. Last updated 5 months ago.
4.9 match 255 stars 12.85 score 684 scripts 27 dependents
prestodb
RPresto:DBI Connector to Presto
Implements a 'DBI' compliant interface to Presto. Presto is an open source distributed SQL query engine for running interactive analytic queries against data sources of all sizes ranging from gigabytes to petabytes: <https://prestodb.io/>.
Maintained by Jarod G.R. Meng. Last updated 1 months ago.
6.5 match 132 stars 9.73 score 25 scripts 4 dependents
djvanderlaan
LaF:Fast Access to Large ASCII Files
Methods for fast access to large ASCII files. Currently the following file formats are supported: comma separated format (CSV) and fixed width format. It is assumed that the files are too large to fit into memory, although the package can also be used to efficiently access files that do fit into memory. Methods are provided to access and process files blockwise. Furthermore, an opened file can be accessed as one would an ordinary data.frame. The LaF vignette gives an overview of the functionality provided.
Maintained by Jan van der Laan. Last updated 3 months ago.
7.1 match 54 stars 8.62 score 61 scripts 5 dependents
cynkra
dm:Relational Data Models
Provides tools for working with multiple related tables, stored as data frames or in a relational database. Multiple tables (data and metadata) are stored in a compound object, which can then be manipulated with a pipe-friendly syntax.
Maintained by Kirill Müller. Last updated 2 months ago.
data-modeldata-warehousingdatawarehousingdbidbplyrrelational-databases
4.0 match 511 stars 14.81 score 410 scripts 8 dependentsrstudio
blastula:Easily Send HTML Email Messages
Compose and send out responsive HTML email messages that render perfectly across a range of email clients and device sizes. Helper functions let the user insert embedded images, web link buttons, and 'ggplot2' plot objects into the message body. Messages can be sent through an 'SMTP' server, through the 'Posit Connect' service, or through the 'Mailgun' API service <https://www.mailgun.com/>.
Maintained by Richard Iannone. Last updated 8 months ago.
easy-to-useemailhtmlmarkdownresponsive-emailsmtp
5.7 match 552 stars 10.27 score 348 scripts 5 dependentsrstudio
renv:Project Environments
A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.
Maintained by Kevin Ushey. Last updated 3 days ago.
3.1 match 1.0k stars 18.55 score 1.5k scripts 113 dependents
pepijn-devries
adfExplorer:Access and Manipulate Amiga Disk Files
Amiga Disk Files (ADF) are virtual representations of 3.5 inch floppy disks for the Commodore Amiga. Most disk drives from other systems (including modern drives) are not able to read these disks. The 'adfExplorer' package enables you to establish R connections to files on such virtual DOS-formatted disks, which can be use to read from and write to those files.
Maintained by Pepijn de Vries. Last updated 2 months ago.
9.8 match 3 stars 5.94 score 36 scriptsbioc
biodb:biodb, a library and a development framework for connecting to chemical and biological databases
The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.
Maintained by Pierrick Roger. Last updated 5 months ago.
softwareinfrastructuredataimportkeggbiologycheminformaticschemistrydatabasescpp
7.3 match 11 stars 7.85 score 24 scripts 6 dependentsbioc
Biobase:Biobase: Base functions for Bioconductor
Functions that are needed by many other packages or which replace R functions.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
infrastructurebioconductor-packagecore-package
3.5 match 9 stars 16.45 score 6.6k scripts 1.8k dependents
edjnet
tidywikidatar:Explore 'Wikidata' Through Tidy Data Frames
Query 'Wikidata' API <https://www.wikidata.org/wiki/Wikidata:Main_Page> with ease, get tidy data frames in response, and cache data in a local database.
Maintained by Giorgio Comai. Last updated 8 months ago.
7.3 match 26 stars 7.86 score 46 scripts 2 dependents
andrewmarx
samc:Spatial Absorbing Markov Chains
Implements functions for working with absorbing Markov chains. The implementation is based on the framework described in "Toward a unified framework for connectivity that disentangles movement and mortality in space and time" by Fletcher et al. (2019) <doi:10.1111/ele.13333>, which applies them to spatial ecology. This framework incorporates both resistance and absorption with spatial absorbing Markov chains (SAMC) to provide several short-term and long-term predictions for metrics related to connectivity in landscapes. Despite the ecological context of the framework, this package can be used in any application of absorbing Markov chains.
Maintained by Andrew Marx. Last updated 5 months ago.
absorbing-markov-chainsconnectivitylandscape-ecologylandscape-metricsmarkov-chaincpp
10.8 match 12 stars 5.26 score 15 scriptsr-lib
ps:List, Query, Manipulate System Processes
List, query and manipulate all system processes, on 'Windows', 'Linux' and 'macOS'.
Maintained by Gábor Csárdi. Last updated 16 days ago.
3.8 match 79 stars 15.09 score 108 scripts 1.5k dependents
tidyverse
ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics
A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.
Maintained by Thomas Lin Pedersen. Last updated 9 days ago.
data-visualisationvisualisation
2.3 match 6.6k stars 25.10 score 645k scripts 7.5k dependents
christopherkenny
geomander:Geographic Tools for Studying Gerrymandering
A compilation of tools to complete common tasks for studying gerrymandering. This focuses on the geographic tool side of common problems, such as linking different levels of spatial units or estimating how to break up units. Functions exist for creating redistricting-focused data for the US.
Maintained by Christopher T. Kenny. Last updated 18 days ago.
7.2 match 14 stars 7.81 score 191 scripts 1 dependentsr-dbi
RPostgres:C++ Interface to PostgreSQL
Fully DBI-compliant C++-backed interface to PostgreSQL <https://www.postgresql.org/>, an open-source relational database.
Maintained by Kirill Müller. Last updated 20 days ago.
3.8 match 338 stars 14.78 score 1.6k scripts 31 dependents
datashield
DSI:'DataSHIELD' Interface
'DataSHIELD' is an infrastructure and series of R packages that enables the remote and 'non-disclosive' analysis of sensitive research data. This package defines the API that is to be implemented by 'DataSHIELD' compliant data repositories.
Maintained by Yannick Marcon. Last updated 4 months ago.
8.0 match 2 stars 7.01 score 106 scripts 4 dependents
cboettig
duckdbfs:High Performance Remote File System, Database and 'Geospatial' Access Using 'duckdb'
Provides friendly wrappers for creating 'duckdb'-backed connections to tabular datasets ('csv', parquet, etc) on local or remote file systems. This mimics the behaviour of "open_dataset" in the 'arrow' package, but in addition to 'S3' file system also generalizes to any list of 'http' URLs.
Maintained by Carl Boettiger. Last updated 5 days ago.
6.4 match 85 stars 8.51 score 41 scripts 16 dependents
mlverse
pysparklyr:Provides a 'PySpark' Back-End for the 'sparklyr' Package
It enables 'sparklyr' to integrate with 'Spark Connect', and 'Databricks Connect' by providing a wrapper over the 'PySpark' 'python' library.
Maintained by Edgar Ruiz. Last updated 3 days ago.
databrickspysparksparkspark-connect
10.2 match 15 stars 5.33 score 13 scripts
fawda123
NeuralNetTools:Visualization and Analysis Tools for Neural Networks
Visualization and analysis tools to aid in the interpretation of neural network models. Functions are available for plotting, quantifying variable importance, conducting a sensitivity analysis, and obtaining a simple list of model weights.
Maintained by Marcus W. Beck. Last updated 3 years ago.
5.6 match 72 stars 9.61 score 530 scripts 6 dependents
louisaslett
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.
13.7 match 7 stars 3.92 score 12 scriptsbioc
Rcpi:Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.
Maintained by Nan Xiao. Last updated 5 months ago.
softwaredataimportdatarepresentationfeatureextractioncheminformaticsbiomedicalinformaticsproteomicsgosystemsbiologybioconductorbioinformaticsdrug-discoveryfeature-extractionfingerprintmolecular-descriptorsprotein-sequences
6.9 match 37 stars 7.81 score 29 scripts
rblp
Rblpapi:R Interface to 'Bloomberg'
An R Interface to 'Bloomberg' is provided via the 'Blp API'.
Maintained by Dirk Eddelbuettel. Last updated 4 days ago.
5.7 match 169 stars 9.43 score 115 scriptsrstudio
plumbertableau:Turn 'Plumber' APIs into 'Tableau' Extensions
Build 'Plumber' APIs that can be used in 'Tableau' workbooks. Annotations in R comments allow APIs to conform to the 'Tableau Analytics Extension' specification, so that R code can be used to power 'Tableau' workbooks.
Maintained by James Blair. Last updated 1 years ago.
7.8 match 30 stars 6.74 score 23 scriptsropensci
elastic:General Purpose Interface to 'Elasticsearch'
Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java' Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' API (<https://www.elastic.co/elasticsearch/>), including functions for setting connection details to 'Elasticsearch' instances, loading bulk data, searching for documents with both 'HTTP' query variables and 'JSON' based body requests. In addition, 'elastic' provides functions for interacting with API's for 'indices', documents, nodes, clusters, an interface to the cat API, and more.
Maintained by Scott Chamberlain. Last updated 2 years ago.
databaseelasticsearchhttpapisearchnosqljavajsondocumentsdata-sciencedatabase-wrapperetl
5.9 match 247 stars 8.98 score 151 scripts 1 dependents
benubah
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.
8.9 match 19 stars 5.86 score 76 scriptsmlverse
chattr:Interact with Large Language Models in 'RStudio'
Enables user interactivity with large-language models ('LLM') inside the 'RStudio' integrated development environment (IDE). The user can interact with the model using the 'shiny' app included in this package, or directly in the 'R' console. It comes with back-ends for 'OpenAI', 'GitHub' 'Copilot', and 'LlamaGPT'.
Maintained by Edgar Ruiz. Last updated 2 months ago.
4.9 match 215 stars 10.55 score 71 scripts 1 dependentsropensci
rotl:Interface to the 'Open Tree of Life' API
An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.
Maintained by Francois Michonneau. Last updated 2 years ago.
metadataropensciphylogeneticsindependant-contrastsbiodiversitypeer-reviewedphylogenytaxonomy
4.3 match 40 stars 12.05 score 356 scripts 29 dependents
kangjian2016
brainKCCA:Region-Level Connectivity Network Construction via Kernel Canonical Correlation Analysis
It is designed to calculate connection between (among) brain regions and plot connection lines. Also, the summary function is included to summarize group-level connectivity network. Kang, Jian (2016) <doi:10.1016/j.neuroimage.2016.06.042>.
Maintained by Jian Kang. Last updated 6 years ago.
13.7 match 3.70 score 5 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.
6.8 match 4 stars 7.38 score 9 scripts 3 dependentsr-dbi
RMySQL:Database Interface and 'MySQL' Driver for R
Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code ported from S-PLUS. A modern 'MySQL' client written in 'C++' is available from the 'RMariaDB' package.
Maintained by Jeroen Ooms. Last updated 1 months ago.
3.7 match 209 stars 13.68 score 3.7k scripts 15 dependents
poissonconsulting
readwritesqlite:Enhanced Reading and Writing for 'SQLite' Databases
Reads and writes data frames to 'SQLite' databases while preserving time zones (for POSIXct columns), projections (for 'sfc' columns), units (for 'units' columns), levels (for factors and ordered factors) and classes for logical, Date and 'hms' columns. It also logs changes to tables and provides more informative error messages.
Maintained by Joe Thorley. Last updated 2 months ago.
dbilogmetadataposixctreadsfcsqliteunitswrite
7.8 match 38 stars 6.42 score 11 scripts 1 dependents
jwijffels
ETLUtils:Utility Functions to Execute Standard Extract/Transform/Load Operations (using Package 'ff') on Large Data
Provides functions to facilitate the use of the 'ff' package in interaction with big data in 'SQL' databases (e.g. in 'Oracle', 'MySQL', 'PostgreSQL', 'Hive') by allowing easy importing directly into 'ffdf' objects using 'DBI', 'RODBC' and 'RJDBC'. Also contains some basic utility functions to do fast left outer join merging based on 'match', factorisation of data and a basic function for re-coding vectors.
Maintained by Jan Wijffels. Last updated 5 years ago.
10.5 match 20 stars 4.75 score 28 scriptscran
datarobot:'DataRobot' Predictive Modeling API
For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Maintained by AJ Alon. Last updated 1 years ago.
14.1 match 2 stars 3.48 scorerstudio
config:Manage Environment Specific Configuration Values
Manage configuration values across multiple environments (e.g. development, test, production). Read values using a function that determines the current environment and returns the appropriate value.
Maintained by Andrie de Vries. Last updated 2 months ago.
3.1 match 261 stars 15.69 score 1.8k scripts 202 dependents
oobianom
r2social:Seamless Integration of Sharing and Connect Buttons in Markdown and Apps
Implementation of 'JQuery' <https://jquery.com> and 'CSS' styles to allow easy incorporation of various social media elements on a page. The elements include addition of share buttons or connect with us buttons or hyperlink buttons to 'Shiny' applications or dashboards and 'Rmarkdown' documents.Sharing capability on social media platforms including 'Facebook' <https://www.facebook.com>, 'Linkedin' <https://www.linkedin.com>, 'X/Twitter' <https://x.com>, 'Tumblr' <https://www.tumblr.com>, 'Pinterest' <https://www.pinterest.com>, 'Whatsapp' <https://www.whatsapp.com>, 'Reddit' <https://www.reddit.com>, 'Baidu' <https://www.baidu.com>, 'Blogger' <https://www.blogger.com>, 'Weibo' <https://www.weibo.com>, 'Instagram' <https://www.instagram.com>, 'Telegram' <https://www.telegram.me>, 'Youtube' <https://www.youtube.com>.
Maintained by Obinna Obianom. Last updated 8 months ago.
9.0 match 6 stars 5.42 score 29 scripts
munterfi
hereR:'sf'-Based Interface to the 'HERE' REST APIs
Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>: (1) geocode and autosuggest addresses or reverse geocode POIs using the 'Geocoder' API; (2) route directions, travel distance or time matrices and isolines using the 'Routing', 'Matrix Routing' and 'Isoline Routing' APIs; (3) request real-time traffic flow and incident information from the 'Traffic' API; (4) find request public transport connections and nearby stations from the 'Public Transit' API; (5) request intermodal routes using the 'Intermodal Routing' API; (6) get weather forecasts, reports on current weather conditions, astronomical information and alerts at a specific location from the 'Destination Weather' API. Locations, routes and isolines are returned as 'sf' objects.
Maintained by Merlin Unterfinger. Last updated 24 days ago.
apigeocodinggishere-technologiesisolineroutingrspatialtrafficweather
5.5 match 90 stars 8.70 score 63 scripts
azure
AzureRMR:Interface to 'Azure Resource Manager'
A lightweight but powerful R interface to the 'Azure Resource Manager' REST API. The package exposes a comprehensive class framework and related tools for creating, updating and deleting 'Azure' resource groups, resources and templates. While 'AzureRMR' can be used to manage any 'Azure' service, it can also be extended by other packages to provide extra functionality for specific services. Part of the 'AzureR' family of packages.
Maintained by Hong Ooi. Last updated 1 years ago.
azureazure-resource-managerazure-sdk-rcloud
4.8 match 20 stars 9.94 score 51 scripts 12 dependentscboettig
neonstore:NEON Data Store
The National Ecological Observatory Network (NEON) provides access to its numerous data products through its REST API, <https://data.neonscience.org/data-api/>. This package provides a high-level user interface for downloading and storing NEON data products. Unlike 'neonUtilities', this package will avoid repeated downloading, provides persistent storage, and improves performance. 'neonstore' can also construct a local 'duckdb' database of stacked tables, making it possible to work with tables that are far to big to fit into memory.
Maintained by Carl Boettiger. Last updated 11 months ago.
databaseecologyneon-dataprovenance
7.1 match 9 stars 6.67 score 143 scripts 11 dependents
jsta
nhdR:Tools for Working with the National Hydrography Dataset
Tools for working with the National Hydrography Dataset, with functions for querying, downloading, and networking both the NHD <https://www.usgs.gov/national-hydrography> and NHDPlus <https://www.epa.gov/waterdata/nhdplus-national-hydrography-dataset-plus> datasets.
Maintained by Jemma Stachelek. Last updated 2 years ago.
geospatialnational-hydrography-datasetnhdwater-qualitywater-resources
7.2 match 38 stars 6.48 score 53 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 4 days ago.
3.4 match 845 stars 13.57 score 264 scripts 2 dependents
allanvc
mRpostman:An IMAP Client for R
An easy-to-use IMAP client that provides tools for message searching, selective fetching of message attributes, mailbox management, attachment extraction, and several other IMAP features, paving the way for e-mail data analysis in R.
Maintained by Allan Quadros. Last updated 6 months ago.
7.7 match 31 stars 5.92 score 18 scriptsr-dbi
RMariaDB:Database Interface and MariaDB Driver
Implements a DBI-compliant interface to MariaDB (<https://mariadb.org/>) and MySQL (<https://www.mysql.com/>) databases.
Maintained by Kirill Müller. Last updated 20 days ago.
3.7 match 134 stars 12.36 score 792 scripts 11 dependents
patzaw
TKCat:Tailored Knowledge Catalog
Facilitate the management of data from knowledge resources that are frequently used alone or together in research environments. In 'TKCat', knowledge resources are manipulated as modeled database (MDB) objects. These objects provide access to the data tables along with a general description of the resource and a detail data model documenting the tables, their fields and their relationships. These MDBs are then gathered in catalogs that can be easily explored an shared. Finally, 'TKCat' provides tools to easily subset, filter and combine MDBs and create new catalogs suited for specific needs.
Maintained by Patrice Godard. Last updated 1 days ago.
7.4 match 5 stars 6.08 score 27 scriptsrstudio
tfprobability:Interface to 'TensorFlow Probability'
Interface to 'TensorFlow Probability', a 'Python' library built on 'TensorFlow' that makes it easy to combine probabilistic models and deep learning on modern hardware ('TPU', 'GPU'). 'TensorFlow Probability' includes a wide selection of probability distributions and bijectors, probabilistic layers, variational inference, Markov chain Monte Carlo, and optimizers such as Nelder-Mead, BFGS, and SGLD.
Maintained by Tomasz Kalinowski. Last updated 3 years ago.
5.2 match 54 stars 8.63 score 221 scripts 3 dependents
snoweye
pbdZMQ:Programming with Big Data -- Interface to 'ZeroMQ'
'ZeroMQ' is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus on interactive client/server programming frameworks. For convenience, a minimal 'ZeroMQ' library (4.2.2) is shipped with 'pbdZMQ', which can be used if no system installation of 'ZeroMQ' is available. A few wrapper functions compatible with 'rzmq' are also provided.
Maintained by Wei-Chen Chen. Last updated 6 months ago.
4.5 match 17 stars 9.92 score 46 scripts 26 dependents
shikokuchuo
mirai:Minimalist Async Evaluation Framework for R
Designed for simplicity, a 'mirai' evaluates an R expression asynchronously in a parallel process, locally or distributed over the network. The result is automatically available upon completion. Modern networking and concurrency, built on 'nanonext' and 'NNG' (Nanomsg Next Gen), ensures reliable and efficient scheduling over fast inter-process communications or TCP/IP secured by TLS. Distributed computing can launch remote resources via SSH or cluster managers. An inherently queued architecture handles many more tasks than available processes, and requires no storage on the file system. Innovative features include support for otherwise non-exportable reference objects, event-driven promises, and asynchronous parallel map.
Maintained by Charlie Gao. Last updated 2 days ago.
asyncasynchronous-tasksconcurrencydistributed-computinghigh-performance-computingparallel-computing
3.7 match 217 stars 11.94 score 130 scripts 7 dependents
langcog
childesr:Accessing the 'CHILDES' Database
Tools for connecting to 'CHILDES', an open repository for transcripts of parent-child interaction. For more information on the underlying data, see <https://langcog.github.io/childes-db-website/>.
Maintained by Mika Braginsky. Last updated 3 years ago.
6.6 match 14 stars 6.70 score 102 scripts
hturner
PlackettLuce:Plackett-Luce Models for Rankings
Functions to prepare rankings data and fit the Plackett-Luce model jointly attributed to Plackett (1975) <doi:10.2307/2346567> and Luce (1959, ISBN:0486441369). The standard Plackett-Luce model is generalized to accommodate ties of any order in the ranking. Partial rankings, in which only a subset of items are ranked in each ranking, are also accommodated in the implementation. Disconnected/weakly connected networks implied by the rankings may be handled by adding pseudo-rankings with a hypothetical item. Optionally, a multivariate normal prior may be set on the log-worth parameters and ranker reliabilities may be incorporated as proposed by Raman and Joachims (2014) <doi:10.1145/2623330.2623654>. Maximum a posteriori estimation is used when priors are set. Methods are provided to estimate standard errors or quasi-standard errors for inference as well as to fit Plackett-Luce trees. See the package website or vignette for further details.
Maintained by Heather Turner. Last updated 2 years ago.
plackett-luce-modelspreferencesrankingrankings-datastatistical-models
5.5 match 20 stars 7.97 score 86 scripts 3 dependentsbioc
hermes:Preprocessing, analyzing, and reporting of RNA-seq data
Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom differential expression analyses are available.
Maintained by Daniel Sabanés Bové. Last updated 5 months ago.
rnaseqdifferentialexpressionnormalizationpreprocessingqualitycontrolrna-seqstatistical-engineering
5.6 match 11 stars 7.77 score 48 scripts 1 dependents
hrbrmstr
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
3.4 match 674 stars 12.59 score 2.3k scripts 7 dependents
sweinand
pricelevels:Spatial Price Level Comparisons
Price comparisons within or between countries provide an overall measure of the relative difference in prices, often denoted as price levels. This package provides index number methods for such price comparisons (e.g., The World Bank, 2011, <doi:10.1596/978-0-8213-9728-2>). Moreover, it contains functions for sampling and characterizing price data.
Maintained by Sebastian Weinand. Last updated 10 months ago.
index-numbersprice-comparisonspatial-analysis
10.0 match 4.30 score 2 scriptsthinkr-open
lozen:Management tools for missions
Management tools for missions (internal and external). Includes weekly, GL projects, etc.
Maintained by Sébastien Rochette. Last updated 12 months ago.
8.0 match 7 stars 5.42 score 14 scriptsbioc
biodbNci:biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database
The biodbNci library is an extension of the biodb framework package. It provides access to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database. It allows to retrieve entries by their accession number, and run specific web services.
Maintained by Pierrick Roger. Last updated 5 months ago.
softwareinfrastructuredataimportcpp
10.8 match 4.00 score 2 scriptsr-lib
processx:Execute and Control System Processes
Tools to run system processes in the background. It can check if a background process is running; wait on a background process to finish; get the exit status of finished processes; kill background processes. It can read the standard output and error of the processes, using non-blocking connections. 'processx' can poll a process for standard output or error, with a timeout. It can also poll several processes at once.
Maintained by Gábor Csárdi. Last updated 22 days ago.
2.8 match 235 stars 15.53 score 340 scripts 1.4k dependents
hugaped
MBNMAdose:Dose-Response MBNMA Models
Fits Bayesian dose-response model-based network meta-analysis (MBNMA) that incorporate multiple doses within an agent by modelling different dose-response functions, as described by Mawdsley et al. (2016) <doi:10.1002/psp4.12091>. By modelling dose-response relationships this can connect networks of evidence that might otherwise be disconnected, and can improve precision on treatment estimates. Several common dose-response functions are provided; others may be added by the user. Various characteristics and assumptions can be flexibly added to the models, such as shared class effects. The consistency of direct and indirect evidence in the network can be assessed using unrelated mean effects models and/or by node-splitting at the treatment level.
Maintained by Hugo Pedder. Last updated 1 months ago.
6.5 match 10 stars 6.60 score
scasanova
f1dataR:Access Formula 1 Data
Obtain Formula 1 data via the 'Jolpica API' <https://jolpi.ca> and the unofficial API <https://www.formula1.com/en/timing/f1-live> via the 'fastf1' 'Python' library <https://docs.fastf1.dev/>.
Maintained by Santiago Casanova. Last updated 15 days ago.
5.3 match 58 stars 7.96 score 26 scriptskwb-r
r2q:Connectable Separate Sewer System to Small Surface Waters - An Immission Based Assessment
The R package is used to define a tolerable pollutant input into small surface waters via rainwater runoff. It assigns a maximal connectable urban area to the surface water. For planning areas, different scenarios regarding the connection of surfaces to the separate sewer system and runoff water treatment can be calculated.
Maintained by Malte Zamzow. Last updated 2 years ago.
10.6 match 4.00 score 2 scriptscedricbriandgithub
stacomirtools:Connection Class for Package stacomiR
S4 class wrappers for the 'ODBC' and Pool DBI connection, also provides some utilities to paste small datasets to clipboard, rename columns. It is used by the package 'stacomiR' for connections to the database. Development versions of 'stacomiR' are available in R-forge.
Maintained by Cedric Briand. Last updated 3 years ago.
17.8 match 2.35 score 15 scripts 1 dependents
urbananalyst
dodgr:Distances on Directed Graphs
Distances on dual-weighted directed graphs using priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>). Weighted directed graphs have weights from A to B which may differ from those from B to A. Dual-weighted directed graphs have two sets of such weights. A canonical example is a street network to be used for routing in which routes are calculated by weighting distances according to the type of way and mode of transport, yet lengths of routes must be calculated from direct distances.
Maintained by Mark Padgham. Last updated 5 days ago.
distanceopenstreetmaproutershortest-pathsstreet-networkscpp
3.6 match 129 stars 11.53 score 229 scripts 4 dependents
vpihur
clValid:Validation of Clustering Results
Statistical and biological validation of clustering results. This package implements Dunn Index, Silhouette, Connectivity, Stability, BHI and BSI. Further information can be found in Brock, G et al. (2008) <doi: 10.18637/jss.v025.i04>.
Maintained by Vasyl Pihur. Last updated 4 years ago.
5.8 match 5 stars 7.19 score 422 scripts 14 dependents
tomoakin
RPostgreSQL:R Interface to the 'PostgreSQL' Database System
Database interface and 'PostgreSQL' driver for 'R'. This package provides a Database Interface 'DBI' compliant driver for 'R' to access 'PostgreSQL' database systems. In order to build and install this package from source, 'PostgreSQL' itself must be present your system to provide 'PostgreSQL' functionality via its libraries and header files. These files are provided as 'postgresql-devel' package under some Linux distributions. On 'macOS' and 'Microsoft Windows' system the attached 'libpq' library source will be used.
Maintained by Tomoaki Nishiyama. Last updated 1 years ago.
3.6 match 65 stars 11.52 score 4.5k scripts 19 dependentsropensci
DataSpaceR:Interface to 'the CAVD DataSpace'
Provides a convenient API interface to access immunological data within 'the CAVD DataSpace'(<https://dataspace.cavd.org>), a data sharing and discovery tool that facilitates exploration of HIV immunological data from pre-clinical and clinical HIV vaccine studies.
Maintained by Jason Taylor. Last updated 24 days ago.
6.2 match 5 stars 6.72 score 42 scripts
derek-corcoran-barrios
NetworkExtinction:Extinction Simulation in Ecological Networks
Simulates the extinction of species in ecological networks and it analyzes its cascading effects, described in Dunne et al. (2002) <doi:10.1073/pnas.192407699>.
Maintained by Derek Corcoran. Last updated 4 months ago.
8.0 match 5 stars 5.15 score 19 scripts
shixiangwang
ggpolar:Dots and Their Connections in Polar Coordinate System
Provides basic graphing functions to fully demonstrate point-to-point connections in a polar coordinate space.
Maintained by Shixiang Wang. Last updated 2 years ago.
8.8 match 9 stars 4.65 score 7 scripts
giocomai
castarter:Content Analysis Starter Toolkit
Consistent approaches for basic web scraping, text mining and word frequency analysis of textual datasets
Maintained by Giorgio Comai. Last updated 1 days ago.
9.0 match 3 stars 4.52 score 2 scripts
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 4 days ago.
arrayhdfss3storage-managertiledbcpp
3.4 match 107 stars 11.96 score 306 scripts 4 dependentsropensci
rzmq:R Bindings for 'ZeroMQ'
Interface to the 'ZeroMQ' lightweight messaging kernel (see <https://zeromq.org/> for more information).
Maintained by Jeroen Ooms. Last updated 3 months ago.
5.6 match 84 stars 7.08 score 81 scriptsbioc
netZooR:Unified methods for the inference and analysis of gene regulatory networks
netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.
Maintained by Tara Eicher. Last updated 9 days ago.
networkinferencenetworkgeneregulationgeneexpressiontranscriptionmicroarraygraphandnetworkgene-regulatory-networktranscription-factors
4.9 match 105 stars 7.98 score
asalavaty
influential:Identification and Classification of the Most Influential Nodes
Contains functions for the classification and ranking of top candidate features, reconstruction of networks from adjacency matrices and data frames, analysis of the topology of the network and calculation of centrality measures, and identification of the most influential nodes. Also, a function is provided for running SIRIR model, which is the combination of leave-one-out cross validation technique and the conventional SIR model, on a network to unsupervisedly rank the true influence of vertices. Additionally, some functions have been provided for the assessment of dependence and correlation of two network centrality measures as well as the conditional probability of deviation from their corresponding means in opposite direction. Fred Viole and David Nawrocki (2013, ISBN:1490523995). Csardi G, Nepusz T (2006). "The igraph software package for complex network research." InterJournal, Complex Systems, 1695. Adopted algorithms and sources are referenced in function document.
Maintained by Adrian Salavaty. Last updated 5 months ago.
centrality-measuresclassification-modelinfluence-rankingnetwork-analysispriaritization-model
6.0 match 27 stars 6.54 score 43 scripts 1 dependents
ineelhere
clintrialx:Connect and Work with Clinical Trials Data Sources
Are you spending too much time fetching and managing clinical trial data? Struggling with complex queries and bulk data extraction? What if you could simplify this process with just a few lines of code? Introducing 'clintrialx' - Fetch clinical trial data from sources like 'ClinicalTrials.gov' <https://clinicaltrials.gov/> and the 'Clinical Trials Transformation Initiative - Access to Aggregate Content of ClinicalTrials.gov' database <https://aact.ctti-clinicaltrials.org/>, supporting pagination and bulk downloads. Also, you can generate HTML reports based on the data obtained from the sources!
Maintained by Indraneel Chakraborty. Last updated 5 days ago.
aactbioinformaticsclinical-dataclinical-trialsclinicaltrialsgovcttidatadata-managementmedical-informaticsr-languagetrials
6.8 match 15 stars 5.76 score 11 scriptsbioc
cicero:Predict cis-co-accessibility from single-cell chromatin accessibility data
Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends monocle 2 for use in chromatin accessibility data.
Maintained by Hannah Pliner. Last updated 5 months ago.
sequencingclusteringcellbasedassaysimmunooncologygeneregulationgenetargetepigeneticsatacseqsinglecell
6.7 match 5.80 score 312 scriptsr-lib
httr:Tools for Working with URLs and HTTP
Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).
Maintained by Hadley Wickham. Last updated 1 years ago.
1.9 match 989 stars 20.56 score 29k scripts 4.3k dependents
molgenis
DSMolgenisArmadillo:'DataSHIELD' Client for 'MOLGENIS Armadillo'
'DataSHIELD' is an infrastructure and series of R packages that enables the remote and 'non-disclosive' analysis of sensitive research data. This package is the 'DataSHIELD' interface implementation to analyze data shared on a 'MOLGENIS Armadillo' server. 'MOLGENIS Armadillo' is a light-weight 'DataSHIELD' server using a file store and an 'RServe' server.
Maintained by Mariska Slofstra. Last updated 8 months ago.
5.9 match 6.54 score 48 scripts
reichlab
zoltr:Interface to the 'Zoltar' Forecast Repository API
'Zoltar' <https://www.zoltardata.com/> is a website that provides a repository of model forecast results in a standardized format and a central location. It supports storing, retrieving, comparing, and analyzing time series forecasts for prediction challenges of interest to the modeling community. This package provides functions for working with the 'Zoltar' API, including connecting and authenticating, getting meta information (projects, models, and forecasts, and truth), and uploading, downloading, and deleting forecast and truth data.
Maintained by Matthew Cornell. Last updated 10 days ago.
5.1 match 2 stars 7.58 score 175 scripts 3 dependents
rspatial
geodata:Download Geographic Data
Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, crops, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.
Maintained by Robert J. Hijmans. Last updated 1 months ago.
3.5 match 162 stars 10.75 score 1.5k scripts 7 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 Müller. Last updated 25 days ago.
2.0 match 327 stars 18.73 score 8.1k scripts 1.1k dependents
baileych
srcr:Simplify Connections to Database Sources
Connecting to databases requires boilerplate code to specify connection parameters and to set up sessions properly with the DBMS. This package provides a simple tool to fill two purposes: abstracting connection details, including secret credentials, out of your source code and managing configuration for frequently-used database connections in a persistent and flexible way, while minimizing requirements on the runtime environment.
Maintained by Charles Bailey. Last updated 6 days ago.
9.0 match 1 stars 4.18 score 3 scripts
dimitri-justeau
restoptr:Ecological Restoration Planning
Flexible framework for ecological restoration planning. It aims to identify priority areas for restoration efforts using optimization algorithms (based on Justeau-Allaire et al. 2021 <doi:10.1111/1365-2664.13803>). Priority areas can be identified by maximizing landscape indices, such as the effective mesh size (Jaeger 2000 <doi:10.1023/A:1008129329289>), or the integral index of connectivity (Pascual-Hortal & Saura 2006 <doi:10.1007/s10980-006-0013-z>). Additionally, constraints can be used to ensure that priority areas exhibit particular characteristics (e.g., ensure that particular places are not selected for restoration, ensure that priority areas form a single contiguous network). Furthermore, multiple near-optimal solutions can be generated to explore multiple options in restoration planning. The package leverages the 'Choco-solver' software to perform optimization using constraint programming (CP) techniques (<https://choco-solver.org/>).
Maintained by Dimitri Justeau-Allaire. Last updated 8 months ago.
7.4 match 11 stars 5.04 score 6 scriptsposit-dev
connectcreds:Manage 'OAuth' Credentials from 'Posit Connect'
A toolkit for making use of credentials mediated by 'Posit Connect'. It handles the details of communicating with the Connect API correctly, 'OAuth' token caching, and refresh behaviour.
Maintained by Aaron Jacobs. Last updated 1 months ago.
9.2 match 4 stars 4.00 score 1 scriptsinbo
watina:Querying and Processing Data from the INBO Watina Database
The R-package watina contains functions to query and process data from the Watina database at the Research Institute for Nature and Forest (INBO). This database primarily provides groundwater level and chemical data, mainly from natural areas in Flanders (Belgium).
Maintained by Floris Vanderhaeghe. Last updated 4 months ago.
groundwaterpreprocessing-functionsreproducibility
8.9 match 2 stars 4.16 score 24 scripts
dfe-analytical-services
dfeR:Common Department for Education Analysis Tasks
Preferred methods for common analytical tasks that are undertaken across the Department, including number formatting, project templates and curated reference data.
Maintained by Cam Race. Last updated 27 days ago.
5.3 match 12 stars 6.94 score 8 scripts
gforge
Gmisc:Descriptive Statistics, Transition Plots, and More
Tools for making the descriptive "Table 1" used in medical articles, a transition plot for showing changes between categories (also known as a Sankey diagram), flow charts by extending the grid package, a method for variable selection based on the SVD, Bézier lines with arrows complementing the ones in the 'grid' package, and more.
Maintained by Max Gordon. Last updated 2 years ago.
3.5 match 50 stars 10.40 score 233 scripts 2 dependentsrstudio
vetiver:Version, Share, Deploy, and Monitor Models
The goal of 'vetiver' is to provide fluent tooling to version, share, deploy, and monitor a trained model. Functions handle both recording and checking the model's input data prototype, and predicting from a remote API endpoint. The 'vetiver' package is extensible, with generics that can support many kinds of models.
Maintained by Julia Silge. Last updated 5 months ago.
3.5 match 185 stars 10.48 score 466 scripts 1 dependentsr-lib
cli:Helpers for Developing Command Line Interfaces
A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.
Maintained by Gábor Csárdi. Last updated 1 days ago.
1.9 match 664 stars 19.33 score 1.4k scripts 14k dependents
mhahsler
stream:Infrastructure for Data Stream Mining
A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893, NSF CMMI 1728612, and NIH R21HG005912. Hahsler et al (2017) <doi:10.18637/jss.v076.i14>.
Maintained by Michael Hahsler. Last updated 4 days ago.
data-stream-clusteringdatastreamstream-miningcpp
3.6 match 39 stars 10.05 score 132 scripts 3 dependentsbioc
sevenbridges:Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.
Maintained by Phil Webster. Last updated 5 months ago.
softwaredataimportthirdpartyclientapi-clientbioconductorbioinformaticscloudcommon-workflow-languagesevenbridges
4.9 match 35 stars 7.40 score 24 scripts
wilkelab
cowplot:Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.
Maintained by Claus O. Wilke. Last updated 2 months ago.
1.9 match 714 stars 18.83 score 75k scripts 1.4k dependentsshikokuchuo
nanonext:NNG (Nanomsg Next Gen) Lightweight Messaging Library
R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a socket library for reliable, high-performance messaging over in-process, IPC, TCP, WebSocket and secure TLS transports. Implements 'Scalability Protocols', a standard for common communications patterns including publish/subscribe, request/reply and service discovery. As its own threaded concurrency framework, provides a toolkit for asynchronous programming and distributed computing. Intuitive 'aio' objects resolve automatically when asynchronous operations complete, and synchronisation primitives allow R to wait upon events signalled by concurrent threads.
Maintained by Charlie Gao. Last updated 2 days ago.
concurrencyhttpsipc-messagemessaging-librarynngrpcsocket-communicationsynchronization-primitivestcp-protocolwebsocketmbedtls
3.6 match 60 stars 9.81 score 28 scripts 9 dependentsigraph
igraphdata:A Collection of Network Data Sets for the 'igraph' Package
A small collection of various network data sets, to use with the 'igraph' package: the Enron email network, various food webs, interactions in the immunoglobulin protein, the karate club network, Koenigsberg's bridges, visuotactile brain areas of the macaque monkey, UK faculty friendship network, domestic US flights network, etc.
Maintained by Kirill Müller. Last updated 3 months ago.
3.8 match 55 stars 9.37 score 486 scripts 3 dependents
bioboot
bio3d:Biological Structure Analysis
Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Maintained by Barry Grant. Last updated 5 months ago.
4.1 match 5 stars 8.49 score 1.4k scripts 10 dependents
r-spark
sparklyr.flint:Sparklyr Extension for 'Flint'
This sparklyr extension makes 'Flint' time series library functionalities (<https://github.com/twosigma/flint>) easily accessible through R.
Maintained by Edgar Ruiz. Last updated 3 years ago.
apache-sparkdata-analysisdata-miningdata-sciencedistributeddistributed-computingflintremote-clusterssparksparklyrstatistical-analysisstatisticsstatssummarizationsummary-statisticstime-seriestime-series-analysistwosigma-flint
5.4 match 9 stars 6.46 score 54 scriptsr-lib
xml2:Parse XML
Bindings to 'libxml2' for working with XML data using a simple, consistent interface based on 'XPath' expressions. Also supports XML schema validation; for 'XSLT' transformations see the 'xslt' package.
Maintained by Jeroen Ooms. Last updated 3 days ago.
1.9 match 220 stars 18.52 score 6.3k scripts 2.3k dependents
marce10
Rraven:Connecting R and 'Raven' Sound Analysis Software
A tool to exchange data between R and 'Raven' sound analysis software (Cornell Lab of Ornithology). Functions work on data formats compatible with the R package 'warbleR'.
Maintained by Marcelo Araya-Salas. Last updated 2 months ago.
5.8 match 10 stars 6.00 score 50 scripts
chrhennig
prabclus:Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data
Distance-based parametric bootstrap tests for clustering with spatial neighborhood information. Some distance measures, Clustering of presence-absence, abundance and multilocus genetic data for species delimitation, nearest neighbor based noise detection. Genetic distances between communities. Tests whether various distance-based regressions are equal. Try package?prabclus for on overview.
Maintained by Christian Hennig. Last updated 6 months ago.
5.8 match 1 stars 5.99 score 90 scripts 71 dependentsbioc
PSMatch:Handling and Managing Peptide Spectrum Matches
The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.
Maintained by Laurent Gatto. Last updated 5 months ago.
infrastructureproteomicsmassspectrometrymass-spectrometrypeptide-spectrum-matches
4.1 match 3 stars 8.40 score 15 scripts 39 dependentsmhahsler
streamConnect:Connecting Stream Mining Components Using Sockets and Web Services
Adds functionality to connect stream mining components from package stream using sockets and Web services. The package can be used create distributed workflows and create plumber-based Web services which can be deployed on most common cloud services.
Maintained by Michael Hahsler. Last updated 7 months ago.
8.6 match 3 stars 3.95 score 1 scripts
beanumber
etl:Extract-Transform-Load Framework for Medium Data
A predictable and pipeable framework for performing ETL (extract-transform-load) operations on publicly-accessible medium-sized data set. This package sets up the method structure and implements generic functions. Packages that depend on this package download specific data sets from the Internet, clean them up, and import them into a local or remote relational database management system.
Maintained by Benjamin S. Baumer. Last updated 1 years ago.
4.8 match 129 stars 7.17 score 38 scripts 1 dependentschrhennig
fpc:Flexible Procedures for Clustering
Various methods for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Standardisation of cluster validation statistics by random clusterings and comparison between many clustering methods and numbers of clusters based on this. Cluster-wise cluster stability assessment. Methods for estimation of the number of clusters: Calinski-Harabasz, Tibshirani and Walther's prediction strength, Fang and Wang's bootstrap stability. Gaussian/multinomial mixture fitting for mixed continuous/categorical variables. Variable-wise statistics for cluster interpretation. DBSCAN clustering. Interface functions for many clustering methods implemented in R, including estimating the number of clusters with kmeans, pam and clara. Modality diagnosis for Gaussian mixtures. For an overview see package?fpc.
Maintained by Christian Hennig. Last updated 6 months ago.
3.7 match 11 stars 9.25 score 2.6k scripts 70 dependentscran
sna:Tools for Social Network Analysis
A range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.
Maintained by Carter T. Butts. Last updated 6 months ago.
5.0 match 8 stars 6.78 score 94 dependents
jfrench
smerc:Statistical Methods for Regional Counts
Implements statistical methods for analyzing the counts of areal data, with a focus on the detection of spatial clusters and clustering. The package has a heavy emphasis on spatial scan methods, which were first introduced by Kulldorff and Nagarwalla (1995) <doi:10.1002/sim.4780140809> and Kulldorff (1997) <doi:10.1080/03610929708831995>.
Maintained by Joshua French. Last updated 5 months ago.
5.5 match 3 stars 6.11 score 45 scripts 3 dependents
sebastien-plutniak
archeofrag:Spatial Analysis in Archaeology from Refitting Fragments
Methods to analyse spatial units in archaeology from the relationships between refitting fragmented objects scattered in these units (e.g. stratigraphic layers). Graphs are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. Empirical datasets are provided as examples. Documentation about 'archeofrag' is provided by the vignette included in this package, by the accompanying scientific papers: Plutniak (2021, Journal of Archaeological Science, <doi:10.1016/j.jas.2021.105501>) and Plutniak (2022, Journal of Open Source Software, <doi:10.21105/joss.04335>). This package is complemented by a companion GUI application available at <https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/>.
Maintained by Sebastien Plutniak. Last updated 3 hours ago.
archaeological-objectsarchaeological-sciencearchaeologyfragmentationnetwork-analysis
5.3 match 20 stars 6.38 score 10 scripts 1 dependents
nanxstats
protr:Generating Various Numerical Representation Schemes for Protein Sequences
Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) <DOI:10.1093/bioinformatics/btv042>. For full functionality, the software 'ncbi-blast+' is needed, see <https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html> for more information.
Maintained by Nan Xiao. Last updated 6 months ago.
bioinformaticsfeature-engineeringfeature-extractionmachine-learningpeptidesprotein-sequencessequence-analysis
3.4 match 52 stars 10.02 score 173 scripts 3 dependents
surveydown-dev
surveydown:Markdown-Based Surveys Using 'Quarto' and 'shiny'
Generate surveys using markdown and R code chunks. Surveys are composed of two files: a survey.qmd 'Quarto' file defining the survey content (pages, questions, etc), and an app.R file defining a 'shiny' app with global settings (libraries, database configuration, etc.) and server configuration options (e.g., conditional skipping / display, etc.). Survey data collected from respondents is stored in a 'PostgreSQL' database. Features include controls for conditional skip logic (skip to a page based on an answer to a question), conditional display logic (display a question based on an answer to a question), a customizable progress bar, and a wide variety of question types, including multiple choice (single choice and multiple choices), select, text, numeric, multiple choice buttons, text area, and dates. Because the surveys render into a 'shiny' app, designers can also leverage the reactive capabilities of 'shiny' to create dynamic and interactive surveys.
Maintained by John Paul Helveston. Last updated 4 days ago.
markdownpostgrespostgresqlquartoshinyshiny-appsshiny-rsupabasesurveysurveys
4.0 match 96 stars 8.28 score 133 scripts
r-lib
usethis:Automate Package and Project Setup
Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.
Maintained by Jennifer Bryan. Last updated 11 days ago.
1.9 match 869 stars 17.54 score 5.6k scripts 336 dependents
stla
concom:Connected Components of an Undirected Graph
Provides a function for fast computation of the connected components of an undirected graph (though not faster than the components() function of the 'igraph' package) from the edges or the adjacency matrix of the graph. Based on this one, a function to compute the connected components of a triangle 'rgl' mesh is also provided.
Maintained by Stéphane Laurent. Last updated 3 years ago.
12.2 match 1 stars 2.70 score 7 scriptscran
clv:Cluster Validation Techniques
Package contains most of the popular internal and external cluster validation methods ready to use for the most of the outputs produced by functions coming from package "cluster". Package contains also functions and examples of usage for cluster stability approach that might be applied to algorithms implemented in "cluster" package as well as user defined clustering algorithms.
Maintained by Lukasz Nieweglowski. Last updated 1 years ago.
6.9 match 1 stars 4.73 score 148 scripts 17 dependentsazure
AzureStor:Storage Management in 'Azure'
Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/product-categories/storage/>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS). Part of the 'AzureR' family of packages.
Maintained by Hong Ooi. Last updated 2 years ago.
azure-data-lakeazure-sdk-razure-storageazure-storage-blobazure-storage-file
3.0 match 64 stars 10.72 score 298 scripts 4 dependents
eguidotti
RblDataLicense:R Interface to 'Bloomberg Data License'
R interface to access prices and market data with the 'Bloomberg Data License' service from <https://www.bloomberg.com/professional/product/data-license/>. As a prerequisite, a valid Data License from 'Bloomberg' is needed together with the corresponding SFTP credentials and whitelisting of the IP from which accessing the service. This software and its author are in no way affiliated, endorsed, or approved by 'Bloomberg' or any of its affiliates. 'Bloomberg' is a registered trademark.
Maintained by Emanuele Guidotti. Last updated 7 months ago.
bloombergbloomberg-databloomberg-datalicense
6.6 match 14 stars 4.85 score 9 scripts
prioriactions
prioriactions:Multi-Action Conservation Planning
This uses a mixed integer mathematical programming (MIP) approach for building and solving multi-action planning problems, where the goal is to find an optimal combination of management actions that abate threats, in an efficient way while accounting for spatial aspects. Thus, optimizing the connectivity and conservation effectiveness of the prioritized units and of the deployed actions. The package is capable of handling different commercial (gurobi, CPLEX) and non-commercial (symphony, CBC) MIP solvers. Gurobi optimization solver can be installed using comprehensive instructions in the 'gurobi' installation vignette of the prioritizr package (available in <https://prioritizr.net/articles/gurobi_installation_guide.html>). Instead, 'CPLEX' optimization solver can be obtain from IBM CPLEX web page (available here <https://www.ibm.com/es-es/products/ilog-cplex-optimization-studio>). Additionally, the 'rcbc' R package (available at <https://github.com/dirkschumacher/rcbc>) can be used to obtain solutions using the CBC optimization software (<https://github.com/coin-or/Cbc>). Methods used in the package refers to Salgado-Rojas et al. (2020) <doi:10.1016/j.ecolmodel.2019.108901>, Beyer et al. (2016) <doi:10.1016/j.ecolmodel.2016.02.005>, Cattarino et al. (2015) <doi:10.1371/journal.pone.0128027> and Watts et al. (2009) <doi:10.1016/j.envsoft.2009.06.005>. See the prioriactions website for more information, documentations and examples.
Maintained by Jose Salgado-Rojas. Last updated 2 years ago.
conservationconservation-planoptimizationprioritizationthreatscpp
5.9 match 10 stars 5.40 score 6 scripts
r-spatial
stars:Spatiotemporal Arrays, Raster and Vector Data Cubes
Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Maintained by Edzer Pebesma. Last updated 30 days ago.
1.8 match 571 stars 18.27 score 7.2k scripts 137 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
2.7 match 87 stars 11.94 score 238 scripts 12 dependentsr-lib
httr2:Perform HTTP Requests and Process the Responses
Tools for creating and modifying HTTP requests, then performing them and processing the results. 'httr2' is a modern re-imagining of 'httr' that uses a pipe-based interface and solves more of the problems that API wrapping packages face.
Maintained by Hadley Wickham. Last updated 8 days ago.
1.8 match 246 stars 17.66 score 1.9k scripts 1.1k dependents
hubverse-org
hubData:Tools for accessing and working with hubverse data
A set of utility functions for accessing and working with forecast and target data from Infectious Disease Modeling Hubs.
Maintained by Anna Krystalli. Last updated 4 months ago.
5.5 match 3 stars 5.71 score 60 scripts 2 dependents