Showing 144 of total 144 results (show query)
devopifex
communicate:Communicate Between 'Shiny' Client and Server
What the package does (one paragraph).
Maintained by John Coene. Last updated 10 months ago.
61.4 match 23 stars 3.36 score 5 scripts
shikokuchuo
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
8.0 match 60 stars 9.81 score 28 scripts 9 dependents
sebastien-plutniak
archeoViz:Visualisation, Exploration, and Web Communication of Archaeological Spatial Data
An R 'Shiny' application for visual and statistical exploration and web communication of archaeological spatial data, either remains or sites. It offers interactive 3D and 2D visualisations (cross sections and maps of remains, timeline of the work made in a site) which can be exported in SVG and HTML formats. It performs simple spatial statistics (convex hull, regression surfaces, 2D kernel density estimation) and allows exporting data to other online applications for more complex methods. 'archeoViz' can be used offline locally or deployed on a server, either with interactive input of data or with a static data set. Example is provided at <https://analytics.huma-num.fr/archeoviz/en>.
Maintained by Sebastien Plutniak. Last updated 1 months ago.
archaeologyarcheologydata-visualization
8.9 match 19 stars 7.23 score 6 scripts
dietrichson
ProPublicaR:Access Functions for ProPublica's APIs
Provides wrapper functions to access the ProPublica's Congress and Campaign Finance APIs. The Congress API provides near real-time access to legislative data from the House of Representatives, the Senate and the Library of Congress. The Campaign Finance API provides data from United States Federal Election Commission filings and other sources. The API covers summary information for candidates and committees, as well as certain types of itemized data. For more information about these APIs go to: <https://www.propublica.org/datastore/apis>.
Maintained by Aleksander Dietrichson. Last updated 2 years ago.
14.6 match 12 stars 4.38 score 1 scripts
gesistsa
oolong:Create Validation Tests for Automated Content Analysis
Intended to create standard human-in-the-loop validity tests for typical automated content analysis such as topic modeling and dictionary-based methods. This package offers a standard workflow with functions to prepare, administer and evaluate a human-in-the-loop validity test. This package provides functions for validating topic models using word intrusion, topic intrusion (Chang et al. 2009, <https://papers.nips.cc/paper/3700-reading-tea-leaves-how-humans-interpret-topic-models>) and word set intrusion (Ying et al. 2021) <doi:10.1017/pan.2021.33> tests. This package also provides functions for generating gold-standard data which are useful for validating dictionary-based methods. The default settings of all generated tests match those suggested in Chang et al. (2009) and Song et al. (2020) <doi:10.1080/10584609.2020.1723752>.
Maintained by Chung-hong Chan. Last updated 19 days ago.
textanalysistopicmodelingvalidation
7.5 match 54 stars 7.57 score 23 scripts
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
7.1 match 188 stars 7.86 score 107 scripts 3 dependents
bioc
OmnipathR:OmniPath web service client and more
A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).
Maintained by Denes Turei. Last updated 19 days ago.
graphandnetworknetworkpathwayssoftwarethirdpartyclientdataimportdatarepresentationgenesignalinggeneregulationsystemsbiologytranscriptomicssinglecellannotationkeggcomplexesenzyme-ptmnetworksnetworks-biologyomnipathproteinsquarto
5.5 match 126 stars 9.90 score 226 scripts 2 dependents
welch-lab
cytosignal:What the Package Does (One Line, Title Case)
What the package does (one paragraph).
Maintained by Jialin Liu. Last updated 6 days ago.
8.4 match 16 stars 5.95 score 6 scripts
r-lib
lifecycle:Manage the Life Cycle of your Package Functions
Manage the life cycle of your exported functions with shared conventions, documentation badges, and user-friendly deprecation warnings.
Maintained by Lionel Henry. Last updated 26 days ago.
3.1 match 95 stars 15.84 score 54 scripts 14k dependents
robinhankin
hyper2:The Hyperdirichlet Distribution, Mark 2
A suite of routines for the hyperdirichlet distribution and reified Bradley-Terry; supersedes the 'hyperdirichlet' package; uses 'disordR' discipline <doi:10.48550/ARXIV.2210.03856>. To cite in publications please use Hankin 2017 <doi:10.32614/rj-2017-061>, and for Generalized Plackett-Luce likelihoods use Hankin 2024 <doi:10.18637/jss.v109.i08>.
Maintained by Robin K. S. Hankin. Last updated 3 days ago.
7.2 match 5 stars 6.01 score 38 scripts 1 dependents
mschubert
clustermq:Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM, PBS/Torque)
Evaluate arbitrary function calls using workers on HPC schedulers in single line of code. All processing is done on the network without accessing the file system. Remote schedulers are supported via SSH.
Maintained by Michael Schubert. Last updated 25 days ago.
clusterhigh-performance-computinglsfsgeslurmsshzeromq3cpp
4.2 match 149 stars 10.23 score 253 scripts
inseefr
gustave:A User-Oriented Statistical Toolkit for Analytical Variance Estimation
Provides a toolkit for analytical variance estimation in survey sampling. Apart from the implementation of standard variance estimators, its main feature is to help the sampling expert produce easy-to-use variance estimation "wrappers", where systematic operations (linearization, domain estimation) are handled in a consistent and transparent way.
Maintained by Khaled Larbi. Last updated 1 years ago.
official-statisticssamplingsurvey-samplingvariance-estimation
10.4 match 9 stars 3.91 score 18 scripts
fellstat
ipc:Tools for Message Passing Between Processes
Provides tools for passing messages between R processes. Shiny examples are provided showing how to perform useful tasks such as: updating reactive values from within a future, progress bars for long running async tasks, and interrupting async tasks based on user input.
Maintained by Ian E. Fellows. Last updated 2 years ago.
4.9 match 56 stars 6.50 score 38 scripts 1 dependents
dmurdoch
rgl:3D Visualization Using OpenGL
Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Maintained by Duncan Murdoch. Last updated 2 months ago.
graphicsopenglrglwebgllibglulibglvndlibpnglibx11freetypecpp
1.8 match 91 stars 17.49 score 7.3k scripts 300 dependents
sbg
biocompute:Create and Manipulate BioCompute Objects
Tools to create, validate, and export BioCompute Objects described in King et al. (2019) <doi:10.17605/osf.io/h59uh>. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard. A checksum validator and a JSON schema validator are provided. This package also supports exporting BioCompute Objects as JSON, PDF, HTML, or 'Word' documents, and exporting to cloud-based platforms.
Maintained by Soner Koc. Last updated 9 months ago.
biocomputebiocompute-objectsbioinformaticsscience-communicationsevenbridgesstandardizationworkflow
7.5 match 3 stars 4.07 score 13 scripts
matt-dray
r2eng:Translate R Code To An English Sentence
Take an R expression and convert it to English by matching recognised symbols with an opinionated list of English 'translations'. Inspired By Amelia McNamara's useR! 2020 conference talk.
Maintained by Matt Dray. Last updated 11 months ago.
10.0 match 17 stars 2.93 score 6 scripts
rvlenth
emmeans:Estimated Marginal Means, aka Least-Squares Means
Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Maintained by Russell V. Lenth. Last updated 3 days ago.
1.5 match 377 stars 19.19 score 13k scripts 187 dependents
jbgruber
rollama:Communicate with 'Ollama' to Run Large Language Models Locally
Wraps the 'Ollama' <https://ollama.com> API, which can be used to communicate with generative large language models locally.
Maintained by Johannes B. Gruber. Last updated 1 months ago.
3.4 match 110 stars 8.36 score 52 scripts
bio-statistics
ABACUS:Apps Based Activities for Communicating and Understanding Statistics
A set of Shiny apps for effective communication and understanding in statistics. The current version includes properties of normal distribution, properties of sampling distribution, one-sample z and t tests, two samples independent (unpaired) t test and analysis of variance.
Maintained by Mintu Nath. Last updated 4 years ago.
5.2 match 5.18 score 15 scriptsbioc
InterCellar:InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics
InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. Starting from precomputed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore clusters, genes and functions. Finally, based on functional annotation from Gene Ontology and pathway databases, InterCellar implements data-driven analyses to investigate cell-cell communication in one or multiple conditions.
Maintained by Marta Interlandi. Last updated 5 months ago.
softwaresinglecellvisualizationgotranscriptomics
5.2 match 9 stars 4.95 score 7 scripts
r-simmer
simmer:Discrete-Event Simulation for R
A process-oriented and trajectory-based Discrete-Event Simulation (DES) package for R. It is designed as a generic yet powerful framework. The architecture encloses a robust and fast simulation core written in 'C++' with automatic monitoring capabilities. It provides a rich and flexible R API that revolves around the concept of trajectory, a common path in the simulation model for entities of the same type. Documentation about 'simmer' is provided by several vignettes included in this package, via the paper by Ucar, Smeets & Azcorra (2019, <doi:10.18637/jss.v090.i02>), and the paper by Ucar, Hernández, Serrano & Azcorra (2018, <doi:10.1109/MCOM.2018.1700960>); see 'citation("simmer")' for details.
Maintained by Iñaki Ucar. Last updated 6 months ago.
2.0 match 223 stars 11.47 score 440 scripts 6 dependents
cyrillagger
scDiffCom:Differential Analysis of Intercellular Communication from scRNA-Seq Data
Analysis tools to investigate changes in intercellular communication from scRNA-seq data. Using a Seurat object as input, the package infers which cell-cell interactions are present in the dataset and how these interactions change between two conditions of interest (e.g. young vs old). It relies on an internal database of ligand-receptor interactions (available for human, mouse and rat) that have been gathered from several published studies. Detection and differential analyses rely on permutation tests. The package also contains several tools to perform over-representation analysis and visualize the results. See Lagger, C. et al. (2023) <doi:10.1038/s43587-023-00514-x> for a full description of the methodology.
Maintained by Cyril Lagger. Last updated 1 years ago.
5.2 match 21 stars 4.25 score 17 scripts
jiang-junyao
CACIMAR:cross-species analysis of cell identities, markers and regulations
A toolkit to perform cross-species analysis based on scRNA-seq data. CACIMAR contains 5 main features. (1) identify Markers in each cluster. (2) Cell type annotaion (3) identify conserved markers. (4) identify conserved cell types. (5) identify conserved modules of regulatory networks.
Maintained by Junyao Jiang. Last updated 3 months ago.
cross-species-analysisscrna-seq
4.1 match 12 stars 5.26 score 6 scripts
kassambara
datarium:Data Bank for Statistical Analysis and Visualization
Contains data organized by topics: categorical data, regression model, means comparisons, independent and repeated measures ANOVA, mixed ANOVA and ANCOVA.
Maintained by Alboukadel Kassambara. Last updated 30 days ago.
3.4 match 22 stars 6.29 score 358 scripts
ermlab
LightningR:Tools for Communication with Lightning-Viz Server
The purpose of this package is to enable usage of lightningviz server to be accessible from R. The server itself can be found at http://lightning-viz.org/ and is required to work with this package. Package by itself cannot and will not create any visualizations.
Maintained by Kolodziejski Kamil. Last updated 9 years ago.
4.7 match 32 stars 4.51 score 7 scripts
dpmcsuss
iGraphMatch:Tools for Graph Matching
Versatile tools and data for graph matching analysis with various forms of prior information that supports working with 'igraph' objects, matrix objects, or lists of either.
Maintained by Daniel Sussman. Last updated 10 months ago.
graph-algorithmsgraph-matchingcpp
3.6 match 9 stars 5.83 score 9 scripts
ropensci
charlatan:Make Fake Data
Make fake data that looks realistic, supporting addresses, person names, dates, times, colors, coordinates, currencies, digital object identifiers ('DOIs'), jobs, phone numbers, 'DNA' sequences, doubles and integers from distributions and within a range.
Maintained by Roel M. Hogervorst. Last updated 1 months ago.
datadatasetfake-datafakerpeer-reviewed
2.0 match 296 stars 10.06 score 180 scripts 1 dependents
crunch-io
crunch:Crunch.io Data Tools
The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Maintained by Greg Freedman Ellis. Last updated 11 days ago.
1.8 match 9 stars 10.53 score 200 scripts 2 dependents
jonthegeek
fecapi:'OpenFEC' 'API' Client
A client to interact with the 'OpenFEC' 'API' at <https://api.open.fec.gov/developers/>. The 'OpenFEC' 'API' provides programmatic access to campaign finance data stored by the Federal Election Commission.
Maintained by Jon Harmon. Last updated 11 months ago.
7.5 match 3 stars 2.48 score 1 scriptsbioc
dominoSignal:Cell Communication Analysis for Single Cell RNA Sequencing
dominoSignal is a package developed to analyze cell signaling through ligand - receptor - transcription factor networks in scRNAseq data. It takes as input information transcriptomic data, requiring counts, z-scored counts, and cluster labels, as well as information on transcription factor activation (such as from SCENIC) and a database of ligand and receptor pairings (such as from CellPhoneDB). This package creates an object storing ligand - receptor - transcription factor linkages by cluster and provides several methods for exploring, summarizing, and visualizing the analysis.
Maintained by Jacob T Mitchell. Last updated 5 months ago.
systemsbiologysinglecelltranscriptomicsnetwork
2.9 match 5 stars 6.50 score 5 scripts
christopherkenny
congress:Access the Congress.gov API
Download and read data on United States congressional proceedings. Data is read from the Library of Congress's Congress.gov Application Programming Interface (<https://github.com/LibraryOfCongress/api.congress.gov/>). Functions exist for all version 3 endpoints, including for bills, amendments, congresses, summaries, members, reports, communications, nominations, and treaties.
Maintained by Christopher T. Kenny. Last updated 8 months ago.
4.3 match 14 stars 4.35 score 16 scripts
netfacs
NetFACS:Network Applications to Facial Communication Data
Functions to analyze and visualize communication data, based on network theory and resampling methods. Farine, D. R. (2017) <doi:10.1111/2041-210X.12772>; Carsey, T., & Harden, J. (2014) <doi:10.4135/9781483319605>. Primarily targeted at datasets of facial expressions coded with the Facial Action Coding System. Ekman, P., Friesen, W. V., & Hager, J. C. (2002). "Facial action coding system - investigator's guide" <https://www.paulekman.com/facial-action-coding-system/>.
Maintained by Alan V. Rincon. Last updated 11 months ago.
3.5 match 8 stars 5.08 score 5 scripts
ralmond
Proc4:Four Process Assessment Database and Dispatcher
Utilities for working with messages in the four four process architecture as json objects.
Maintained by Russell Almond. Last updated 1 years ago.
assessment-scoringevidence-centered-designmongodb-database
4.5 match 3.95 score 2 dependents
cran
SpaCCI:Spatially Aware Cell-Cell Interaction Analysis
Provides tools for analyzing spatial cell-cell interactions based on ligand-receptor pairs, including functions for local, regional, and global analysis using spatial transcriptomics data. Integrates with databases like 'CellChat' <http://www.cellchat.org/>, 'CellPhoneDB' <https://www.cellphonedb.org/>, 'Cellinker' <https://www.rna-society.org/cellinker/>, 'ICELLNET' <https://github.com/soumelis-lab/ICELLNET>, and 'ConnectomeDB' <https://humanconnectome.org/software/connectomedb/> to identify ligand-receptor pairs, visualize interactions through heatmaps, chord diagrams, and infer interactions on different spatial scales.
Maintained by Li-Ting Ku. Last updated 2 months ago.
10.1 match 1.73 score 18 scripts
epiverse-trace
epiCo:Statistical and Viz Tools for Vector-Borne Diseases in Colombia
Provides statistical and visualization tools for the analysis of demographic indicators, and spatio-temporal behavior and characterization of outbreaks of vector-borne diseases (VBDs) in Colombia. It implements travel times estimated in Bravo-Vega C., Santos-Vega M., & Cordovez J.M. (2022), and the endemic channel method (Bortman, M. (1999) <https://iris.paho.org/handle/10665.2/8562>).
Maintained by Juan D. Umaña. Last updated 2 months ago.
colombiadecision-supportdemographicsepiverseoutbreak-analysissdg-3spatio-temporal-analysisvector-borne-diseases
2.4 match 12 stars 6.94 score 8 scripts
emmanuelcharpentier
patchSynctex:Communication Between Editor and Viewer for Literate Programs
This utility eases the debugging of literate documents ('noweb' files) by patching the synchronization information (the '.synctex(.gz)' file) produced by 'pdflatex' with concordance information produced by 'Sweave' or 'knitr' and 'Sweave' or 'knitr' ; this allows for bilateral communication between a text editor (visualizing the 'noweb' source) and a viewer (visualizing the resultant 'PDF'), thus bypassing the intermediate 'TeX' file.
Maintained by Emmanuel Charpentier. Last updated 8 years ago.
5.3 match 1 stars 3.18 score 30 scripts
appsilon
shiny.telemetry:'Shiny' App Usage Telemetry
Enables instrumentation of 'Shiny' apps for tracking user session events such as input changes, browser type, and session duration. These events can be sent to any of the available storage backends and analyzed using the included 'Shiny' app to gain insights about app usage and adoption.
Maintained by André Veríssimo. Last updated 3 months ago.
1.7 match 67 stars 9.69 score 29 scripts
snoweye
pbdMPI:R Interface to MPI for HPC Clusters (Programming with Big Data Project)
A simplified, efficient, interface to MPI for HPC clusters. It is a derivation and rethinking of the Rmpi package. pbdMPI embraces the prevalent parallel programming style on HPC clusters. Beyond the interface, a collection of functions for global work with distributed data and resource-independent RNG reproducibility is included. It is based on S4 classes and methods.
Maintained by Wei-Chen Chen. Last updated 6 months ago.
2.3 match 2 stars 7.11 score 179 scripts 3 dependents
alexchristensen
NetworkToolbox:Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis
Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershgoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.
Maintained by Alexander Christensen. Last updated 2 years ago.
2.3 match 23 stars 6.99 score 101 scripts 4 dependents
sccmckenzie
sift:Intelligently Peruse Data
Facilitate extraction of key information from common datasets.
Maintained by Scott McKenzie. Last updated 4 years ago.
3.6 match 4.30 score 4 scriptsbioc
PIUMA:Phenotypes Identification Using Mapper from topological data Analysis
The PIUMA package offers a tidy pipeline of Topological Data Analysis frameworks to identify and characterize communities in high and heterogeneous dimensional data.
Maintained by Mattia Chiesa. Last updated 5 months ago.
clusteringgraphandnetworkdimensionreductionnetworkclassification
3.0 match 4 stars 5.08 score 2 scripts
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.
1.8 match 3 stars 8.20 score 7.8k scripts 11 dependents
bnaras
homomorpheR:Homomorphic Computations in R
Homomorphic computations in R for privacy-preserving applications. Currently only the Paillier Scheme is implemented.
Maintained by Balasubramanian Narasimhan. Last updated 3 years ago.
2.5 match 4 stars 5.73 score 18 scripts 1 dependents
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.
3.3 match 1 stars 4.18 score 2 scripts
bartonicek
plotscaper:Explore Your Data with Interactive Figures
A framework for creating interactive figures for data exploration. All plots are automatically linked and support several kinds of interactive features, including selection, zooming, panning, and parameter manipulation. The figures can be interacted with either manually, using a mouse and a keyboard, or by running code from inside an active R session.
Maintained by Adam Bartonicek. Last updated 23 days ago.
1.7 match 16 stars 7.36 score 23 scripts
kzavez
LearnVizLMM:Learning and Communicating Linear Mixed Models Without Data
Summarizes characteristics of linear mixed effects models without data or a fitted model by converting code for fitting lmer() from 'lme4' and lme() from 'nlme' into tables, equations, and visuals. Outputs can be used to learn how to fit linear mixed effects models in 'R' and to communicate about these models in presentations, manuscripts, and analysis plans.
Maintained by Katherine Zavez. Last updated 5 months ago.
3.4 match 3.70 score 2 scripts
hendersontrent
theft:Tools for Handling Extraction of Features from Time Series
Consolidates and calculates different sets of time-series features from multiple 'R' and 'Python' packages including 'Rcatch22' Henderson, T. (2021) <doi:10.5281/zenodo.5546815>, 'feasts' O'Hara-Wild, M., Hyndman, R., and Wang, E. (2021) <https://CRAN.R-project.org/package=feasts>, 'tsfeatures' Hyndman, R., Kang, Y., Montero-Manso, P., Talagala, T., Wang, E., Yang, Y., and O'Hara-Wild, M. (2020) <https://CRAN.R-project.org/package=tsfeatures>, 'tsfresh' Christ, M., Braun, N., Neuffer, J., and Kempa-Liehr A.W. (2018) <doi:10.1016/j.neucom.2018.03.067>, 'TSFEL' Barandas, M., et al. (2020) <doi:10.1016/j.softx.2020.100456>, and 'Kats' Facebook Infrastructure Data Science (2021) <https://facebookresearch.github.io/Kats/>.
Maintained by Trent Henderson. Last updated 1 months ago.
data-visualisationdata-visualizationdimensionality-reductionmachine-learningtime-series
1.7 match 40 stars 7.48 score 50 scripts 1 dependents
themisefth
duet:Analysing Non-Verbal Communication in Dyadic Interactions from Video Data
Analyzes non-verbal communication by processing data extracted from video recordings of dyadic interactions. It supports integration with open source tools, currently limited to 'OpenPose' (Cao et al. (2019) <doi:10.1109/TPAMI.2019.2929257>), converting its outputs into CSV format for further analysis. The package includes functions for data pre-processing, visualization, and computation of motion indices such as velocity, acceleration, and jerkiness (Cook et al. (2013) <doi:10.1093/brain/awt208>), facilitating the analysis of non-verbal cues in paired interactions and contributing to research on human communication dynamics.
Maintained by Themis Efthimiou. Last updated 19 days ago.
3.6 match 3.40 scorecran
SIAtools:'ShinyItemAnalysis' Modules Development Toolkit
A comprehensive suite of functions designed for constructing and managing 'ShinyItemAnalysis' modules, supplemented with detailed guides, ready-to-use templates, linters, and tests. This package allows developers to seamlessly create and integrate one or more modules into their existing packages or to start a new module project from scratch.
Maintained by Jan Netik. Last updated 2 months ago.
3.3 match 3.48 scorebioc
MOSim:Multi-Omics Simulation (MOSim)
MOSim package simulates multi-omic experiments that mimic regulatory mechanisms within the cell, allowing flexible experimental design including time course and multiple groups.
Maintained by Sonia Tarazona. Last updated 5 months ago.
softwaretimecourseexperimentaldesignrnaseqcpp
1.5 match 9 stars 7.46 score 11 scripts
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.
0.5 match 302 stars 20.88 score 19k scripts 2.9k dependentsbioc
scFeatures:scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction
scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor.
Maintained by Yue Cao. Last updated 5 months ago.
cellbasedassayssinglecellspatialsoftwaretranscriptomics
1.8 match 10 stars 5.95 score 15 scriptsbioc
sccomp:Tests differences in cell-type proportion for single-cell data, robust to outliers
A robust and outlier-aware method for testing differences in cell-type proportion in single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.
Maintained by Stefano Mangiola. Last updated 1 days ago.
bayesianregressiondifferentialexpressionsinglecellmetagenomicsflowcytometryspatialbatch-correctioncompositioncytofdifferential-proportionmicrobiomemultilevelproportionsrandom-effectssingle-cellunwanted-variation
1.3 match 99 stars 8.43 score 69 scripts
carloscinelli
NetworkRiskMeasures:Risk Measures for (Financial) Networks
Implements some risk measures for (financial) networks, such as DebtRank, Impact Susceptibility, Impact Diffusion and Impact Fluidity.
Maintained by Carlos Cinelli. Last updated 5 years ago.
2.0 match 68 stars 5.17 score 44 scripts
myaseen208
PSLM2015:Pakistan Social and Living Standards Measurement Survey 2014-15
Data and statistics of Pakistan Social and Living Standards Measurement (PSLM) survey 2014-15 from Pakistan Bureau of Statistics (<http://www.pbs.gov.pk/>).
Maintained by Muhammad Yaseen. Last updated 7 years ago.
3.3 match 3.10 score 25 scripts
huerqiang
prioGene:Candidate Gene Prioritization for Non-Communicable Diseases Based on Functional Information
In gene sequencing methods, the topological features of protein-protein interaction (PPI) networks are often used, such as ToppNet <https://toppgene.cchmc.org>. In this study, a candidate gene prioritization method was proposed for non-communicable diseases considering disease risks transferred between genes in weighted disease PPI networks with weights for nodes and edges based on functional information.
Maintained by Erqiang Hu. Last updated 5 years ago.
graphandnetworkfunctionalgenomicsgeneticsnetwork
3.3 match 3.00 score 10 scripts
azure
AzureKusto:Interface to 'Kusto'/'Azure Data Explorer'
An interface to 'Azure Data Explorer', also known as 'Kusto', a fast, distributed data exploration service from Microsoft: <https://azure.microsoft.com/en-us/products/data-explorer/>. Includes 'DBI' and 'dplyr' interfaces, with the latter modelled after the 'dbplyr' package, whereby queries are translated from R into the native 'KQL' query language and executed lazily. On the admin side, the package extends the object framework provided by 'AzureRMR' to support creation and deletion of databases, and management of database principals. Part of the 'AzureR' family of packages.
Maintained by Alex Kyllo. Last updated 1 years ago.
azureazure-data-explorerazure-sdk-rbig-data-analyticskusto
1.9 match 18 stars 5.19 score 9 scripts
abhirupkgp
dnr:Simulate Dynamic Networks using Exponential Random Graph Models (ERGM) Family
Functions are provided to fit temporal lag models to dynamic networks. The models are build on top of exponential random graph models (ERGM) framework. There are functions for simulating or forecasting networks for future time points. Abhirup Mallik & Zack W. Almquist (2019) Stable Multiple Time Step Simulation/Prediction From Lagged Dynamic Network Regression Models, Journal of Computational and Graphical Statistics, 28:4, 967-979, <DOI: 10.1080/10618600.2019.1594834>.
Maintained by Abhirup Mallik. Last updated 4 years ago.
3.3 match 2.95 score 18 scripts
ddediu
AdhereR:Adherence to Medications
Computation of adherence to medications from Electronic Health care Data and visualization of individual medication histories and adherence patterns. The package implements a set of S3 classes and functions consistent with current adherence guidelines and definitions. It allows the computation of different measures of adherence (as defined in the literature, but also several original ones), their publication-quality plotting, the estimation of event duration and time to initiation, the interactive exploration of patient medication history and the real-time estimation of adherence given various parameter settings. It scales from very small datasets stored in flat CSV files to very large databases and from single-thread processing on mid-range consumer laptops to parallel processing on large heterogeneous computing clusters. It exposes a standardized interface allowing it to be used from other programming languages and platforms, such as Python.
Maintained by Dan Dediu. Last updated 1 years ago.
adherence-to-medicationselectronic-healthcare-datahadoopmedical-databasesmedication-historiespythonsqlvisualisation
1.3 match 28 stars 7.07 score 47 scripts 1 dependents
uclouvain-cbio
scpdata:Single-Cell Proteomics Data Package
The package disseminates mass spectrometry (MS)-based single-cell proteomics (SCP) datasets. The data were collected from published work and formatted using the `scp` data structure. The data sets contain quantitative information at spectrum, peptide and/or protein level for single cells or minute sample amounts.
Maintained by Christophe Vanderaa. Last updated 9 days ago.
experimentdataexpressiondataexperimenthubreproducibleresearchmassspectrometrydataproteomesinglecelldatapackagetypedata
1.7 match 6 stars 5.58 score 16 scripts
hneth
riskyr:Rendering Risk Literacy more Transparent
Risk-related information (like the prevalence of conditions, the sensitivity and specificity of diagnostic tests, or the effectiveness of interventions or treatments) can be expressed in terms of frequencies or probabilities. By providing a toolbox of corresponding metrics and representations, 'riskyr' computes, translates, and visualizes risk-related information in a variety of ways. Adopting multiple complementary perspectives provides insights into the interplay between key parameters and renders teaching and training programs on risk literacy more transparent.
Maintained by Hansjoerg Neth. Last updated 10 months ago.
2x2-matrixbayesian-inferencecontingency-tablerepresentationriskrisk-literacyvisualization
1.3 match 19 stars 7.36 score 80 scripts
djnavarro
jaysire:Build jsPsych Experiments in R
The jaysire package allows the user to build browser based behavioral experiments within R by providing an interface to the jsPsych javascript library.
Maintained by Danielle Navarro. Last updated 4 years ago.
2.0 match 45 stars 4.26 score 27 scriptscran
Linkage:Clustering Communication Networks Using the Stochastic Topic Block Model Through Linkage.fr
It allows to cluster communication networks using the Stochastic Topic Block Model <doi:10.1007/s11222-016-9713-7> by posting jobs through the API of the linkage.fr server, which implements the clustering method. The package also allows to visualize the clustering results returned by the server.
Maintained by Charles Bouveyron. Last updated 3 years ago.
4.9 match 1.70 score 50 scripts
rstudio
tensorflow:R Interface to 'TensorFlow'
Interface to 'TensorFlow' <https://www.tensorflow.org/>, an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop, server, or mobile device with a single 'API'. 'TensorFlow' was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.
Maintained by Tomasz Kalinowski. Last updated 16 days ago.
0.5 match 1.3k stars 15.35 score 3.2k scripts 74 dependentsrstudio
crosstalk:Inter-Widget Interactivity for HTML Widgets
Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). Currently supports linked brushing and filtering.
Maintained by Carson Sievert. Last updated 2 months ago.
0.5 match 292 stars 14.69 score 1.6k scripts 1.5k dependentsbioc
scBubbletree:Quantitative visual exploration of scRNA-seq data
scBubbletree is a quantitative method for the visual exploration of scRNA-seq data, preserving key biological properties such as local and global cell distances and cell density distributions across samples. It effectively resolves overplotting and enables the visualization of diverse cell attributes from multiomic single-cell experiments. Additionally, scBubbletree is user-friendly and integrates seamlessly with popular scRNA-seq analysis tools, facilitating comprehensive and intuitive data interpretation.
Maintained by Simo Kitanovski. Last updated 5 months ago.
visualizationclusteringsinglecelltranscriptomicsrnaseqbig-databigdatascrna-seqscrna-seq-analysisvisualvisual-exploration
1.2 match 6 stars 5.82 score 8 scripts
miyamot0
fxl:'fxl' Single Case Design Charting Package
The 'fxl' Charting package is used to prepare and design single case design figures that are typically prepared in spreadsheet software. With 'fxl', there is no need to leave the R environment to prepare these works and many of the more unique conventions in single case experimental designs can be performed without the need for physically constructing features of plots (e.g., drawing annotations across plots). Support is provided for various different plotting arrangements (e.g., multiple baseline), annotations (e.g., brackets, arrows), and output formats (e.g., svg, rasters).
Maintained by Shawn Gilroy. Last updated 3 months ago.
behavior-analysissingle-case-designvisual-analysis
1.1 match 8 stars 5.46 score 24 scriptsshikokuchuo
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
0.5 match 217 stars 11.94 score 130 scripts 7 dependents
jenineharris
ergmharris:Local Health Department network data set
Data for use with the Sage Introduction to Exponential Random Graph Modeling text by Jenine K. Harris. Network data set consists of 1283 local health departments and the communication links among them along with several attributes.
Maintained by Jenine K. Harris. Last updated 12 years ago.
5.8 match 1.00 scorerstudio
websocket:'WebSocket' Client Library
Provides a 'WebSocket' client interface for R. 'WebSocket' is a protocol for low-overhead real-time communication: <https://en.wikipedia.org/wiki/WebSocket>.
Maintained by Winston Chang. Last updated 8 months ago.
0.5 match 93 stars 10.91 score 51 scripts 49 dependentscran
ATNr:Run Allometric Trophic Networks Models
Implements the differential equations associated to different versions of Allometric Trophic Models (ATN) to estimate the temporal dynamics of species biomasses in food webs. It offers several features to generate synthetic food webs and to parametrise models as well as a wrapper to the ODE solver deSolve.
Maintained by Benoit Gauzens. Last updated 2 years ago.
1.7 match 3.36 score 23 scripts
hrbrmstr
waffle:Create Waffle Chart Visualizations
Square pie charts (a.k.a. waffle charts) can be used to communicate parts of a whole for categorical quantities. To emulate the percentage view of a pie chart, a 10x10 grid should be used with each square representing 1% of the total. Modern uses of waffle charts do not necessarily adhere to this rule and can be created with a grid of any rectangular shape. Best practices suggest keeping the number of categories small, just as should be done when creating pie charts. Tools are provided to create waffle charts as well as stitch them together, and to use glyphs for making isotype pictograms.
Maintained by Bob Rudis. Last updated 1 years ago.
data-visualisationdata-visualizationdatavisualizationggplot2square-pie-chartswaffle-charts
0.5 match 778 stars 10.66 score 1.3k scripts 5 dependents
pecanproject
PEcAn.remote:PEcAn Model Execution Utilities
This package contains utilities for communicating with and executing code on local and remote hosts. In particular, it has PEcAn-specific utilities for starting ecosystem model runs.
Maintained by Rob Kooper. Last updated 2 days ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants
0.5 match 216 stars 9.66 score 13 scripts 32 dependents
agnerf
BiasedUrn:Biased Urn Model Distributions
Statistical models of biased sampling in the form of univariate and multivariate noncentral hypergeometric distributions, including Wallenius' noncentral hypergeometric distribution and Fisher's noncentral hypergeometric distribution. See vignette("UrnTheory") for explanation of these distributions. Literature: Fog, A. (2008a). Calculation Methods for Wallenius' Noncentral Hypergeometric Distribution, Communications in Statistics, Simulation and Computation, 37(2) <doi:10.1080/03610910701790269>. Fog, A. (2008b). Sampling methods for Wallenius’ and Fisher’s noncentral hypergeometric distributions, Communications in Statistics—Simulation and Computation, 37(2) <doi:10.1080/03610910701790236>.
Maintained by Agner Fog. Last updated 9 months ago.
0.8 match 6.58 score 54 scripts 39 dependentscran
SQRL:Enhances Interaction with 'ODBC' Databases
Provides simple and powerful interfaces that facilitate interaction with 'ODBC' data sources. Each data source gets its own unique and dedicated interface, wrapped around 'RODBC'. Communication settings are remembered between queries, and are managed silently in the background. The interfaces support multi-statement 'SQL' scripts, which can be parameterised via metaprogramming structures and embedded 'R' expressions.
Maintained by Mike Lee. Last updated 1 years ago.
2.5 match 2.00 score 9 scripts
chris31415926535
tardis:Text Analysis with Rules and Dictionaries for Inferring Sentiment
Measure text's sentiment with dictionaries and simple rules covering negations and modifiers. User-supplied dictionaries are supported, including Unicode emojis and multi-word tokens, so this package can also be used to study constructs beyond sentiment.
Maintained by Christopher Belanger. Last updated 2 years ago.
1.3 match 2 stars 4.00 score 10 scripts
ndphillips
FFTrees:Generate, Visualise, and Evaluate Fast-and-Frugal Decision Trees
Create, visualize, and test fast-and-frugal decision trees (FFTs) using the algorithms and methods described by Phillips, Neth, Woike & Gaissmaier (2017), <doi:10.1017/S1930297500006239>. FFTs are simple and transparent decision trees for solving binary classification problems. FFTs can be preferable to more complex algorithms because they require very little information, are easy to understand and communicate, and are robust against overfitting.
Maintained by Hansjoerg Neth. Last updated 5 months ago.
0.5 match 135 stars 9.58 score 144 scripts
nealrichardson
httptest:A Test Environment for HTTP Requests
Testing and documenting code that communicates with remote servers can be painful. Dealing with authentication, server state, and other complications can make testing seem too costly to bother with. But it doesn't need to be that hard. This package enables one to test all of the logic on the R sides of the API in your package without requiring access to the remote service. Importantly, it provides three contexts that mock the network connection in different ways, as well as testing functions to assert that HTTP requests were---or were not---made. It also allows one to safely record real API responses to use as test fixtures. The ability to save responses and load them offline also enables one to write vignettes and other dynamic documents that can be distributed without access to a live server.
Maintained by Neal Richardson. Last updated 1 years ago.
0.5 match 82 stars 9.47 score 276 scripts 1 dependentsnealrichardson
httptest2:Test Helpers for 'httr2'
Testing and documenting code that communicates with remote servers can be painful. This package helps with writing tests for packages that use 'httr2'. It enables testing all of the logic on the R sides of the API without requiring access to the remote service, and it also allows recording real API responses to use as test fixtures. The ability to save responses and load them offline also enables writing vignettes and other dynamic documents that can be distributed without access to a live server.
Maintained by Neal Richardson. Last updated 8 months ago.
0.5 match 33 stars 9.37 score 95 scripts 1 dependents
bpfaff
rneos:XML-RPC Interface to NEOS
Within this package the XML-RPC API to NEOS <https://neos-server.org/neos/> is implemented. This enables the user to pass optimization problems to NEOS and retrieve results within R.
Maintained by Bernhard Pfaff. Last updated 5 years ago.
1.9 match 2.54 score 25 scripts 4 dependents
pachadotdev
cpp11armadillo:An 'Armadillo' Interface
Provides function declarations and inline function definitions that facilitate communication between R and the 'Armadillo' 'C++' library for linear algebra and scientific computing. This implementation is detailed in Vargas Sepulveda and Schneider Malamud (2024) <doi:10.48550/arXiv.2408.11074>.
Maintained by Mauricio Vargas Sepulveda. Last updated 26 days ago.
armadillocppcpp11hacktoberfestlinear-algebra
0.5 match 9 stars 9.14 score 1 scripts 16 dependents
reimandlab
ActivePathways:Integrative Pathway Enrichment Analysis of Multivariate Omics Data
Framework for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets. The package uses p-value merging to combine gene- or protein-level signals, followed by ranked hypergeometric tests to determine enriched pathways and processes. Genes can be integrated using directional constraints that reflect how the input datasets are expected interact with one another. This approach allows researchers to interpret a series of omics datasets in the context of known biology and gene function, and discover associations that are only apparent when several datasets are combined. The recent version of the package is part of the following publication: Directional integration and pathway enrichment analysis for multi-omics data. Slobodyanyuk M^, Bahcheli AT^, Klein ZP, Bayati M, Strug LJ, Reimand J. Nature Communications (2024) <doi:10.1038/s41467-024-49986-4>.
Maintained by Juri Reimand. Last updated 8 months ago.
0.5 match 107 stars 8.61 score 35 scripts 2 dependentsropensci
dittodb:A Test Environment for Database Requests
Testing and documenting code that communicates with remote databases can be painful. Although the interaction with R is usually relatively simple (e.g. data(frames) passed to and from a database), because they rely on a separate service and the data there, testing them can be difficult to set up, unsustainable in a continuous integration environment, or impossible without replicating an entire production cluster. This package addresses that by allowing you to make recordings from your database interactions and then play them back while testing (or in other contexts) all without needing to spin up or have access to the database your code would typically connect to.
Maintained by Jonathan Keane. Last updated 11 months ago.
0.5 match 82 stars 8.04 score 49 scripts
oxfordihtm
oxthema:Oxford Colours, Palettes, Fonts, and Themes
Colours, palettes, fonts, and themes based on University of Oxford's visual identity guidelines <https://communications.web.ox.ac.uk/communications-resources/visual-identity/identity-guidelines>.
Maintained by Ernest Guevarra. Last updated 5 months ago.
0.8 match 3 stars 4.91 score 10 scriptsbioc
BioNERO:Biological Network Reconstruction Omnibus
BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations. BioNERO can be used to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) from gene expression data. Additionally, it can be used to explore topological properties of protein-protein interaction (PPI) networks. GCN inference relies on the popular WGCNA algorithm. GRN inference is based on the "wisdom of the crowds" principle, which consists in inferring GRNs with multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average rank for each interaction pair. As all steps of network analyses are included in this package, BioNERO makes users avoid having to learn the syntaxes of several packages and how to communicate between them. Finally, users can also identify consensus modules across independent expression sets and calculate intra and interspecies module preservation statistics between different networks.
Maintained by Fabricio Almeida-Silva. Last updated 5 months ago.
softwaregeneexpressiongeneregulationsystemsbiologygraphandnetworkpreprocessingnetworknetworkinference
0.5 match 27 stars 7.78 score 50 scripts 1 dependentscran
centiserve:Find Graph Centrality Indices
Calculates centrality indices additional to the 'igraph' package centrality functions.
Maintained by Mahdi Jalili. Last updated 8 years ago.
1.9 match 1 stars 2.08 score 1 dependents
kjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 11 months ago.
1.7 match 2.28 score 38 scripts
reviewburner
AnimalSequences:Analyse Animal Sequential Behaviour and Communication
All animal behaviour occurs sequentially. The package has a number of functions to format sequence data from different sources, to analyse sequential behaviour and communication in animals. It also has functions to plot the data and to calculate the entropy of sequences.
Maintained by Alex Mielke. Last updated 6 months ago.
3.5 match 1.00 score
alexisvdb
singleCellHaystack:A Universal Differential Expression Prediction Tool for Single-Cell and Spatial Genomics Data
One key exploratory analysis step in single-cell genomics data analysis is the prediction of features with different activity levels. For example, we want to predict differentially expressed genes (DEGs) in single-cell RNA-seq data, spatial DEGs in spatial transcriptomics data, or differentially accessible regions (DARs) in single-cell ATAC-seq data. 'singleCellHaystack' predicts differentially active features in single cell omics datasets without relying on the clustering of cells into arbitrary clusters. 'singleCellHaystack' uses Kullback-Leibler divergence to find features (e.g., genes, genomic regions, etc) that are active in subsets of cells that are non-randomly positioned inside an input space (such as 1D trajectories, 2D tissue sections, multi-dimensional embeddings, etc). For the theoretical background of 'singleCellHaystack' we refer to our original paper Vandenbon and Diez (Nature Communications, 2020) <doi:10.1038/s41467-020-17900-3> and our update Vandenbon and Diez (Scientific Reports, 2023) <doi:10.1038/s41598-023-38965-2>.
Maintained by Alexis Vandenbon. Last updated 1 years ago.
bioinformaticscite-seqpseudotimescatac-seqsingle-cellspatial-proteomicsspatial-transcriptomicstranscriptomics
0.5 match 81 stars 6.71 score 64 scripts
bjw34032
oro.dicom:Rigorous - DICOM Input / Output
Data input/output functions for data that conform to the Digital Imaging and Communications in Medicine (DICOM) standard, part of the Rigorous Analytics bundle.
Maintained by Brandon Whitcher. Last updated 1 years ago.
0.5 match 1 stars 6.35 score 188 scripts 8 dependents
matherealize
simdata:Generate Simulated Datasets
Generate simulated datasets from an initial underlying distribution and apply transformations to obtain realistic data. Implements the 'NORTA' (Normal-to-anything) approach from Cario and Nelson (1997) and other data generating mechanisms. Simple network visualization tools are provided to facilitate communicating the simulation setup.
Maintained by Michael Kammer. Last updated 3 months ago.
data-generationregressionsimulationstatistics
0.5 match 7 stars 6.10 score 10 scripts 1 dependents
ganglilab
genekitr:Gene Analysis Toolkit
Provides features for searching, converting, analyzing, plotting, and exporting data effortlessly by inputting feature IDs. Enables easy retrieval of feature information, conversion of ID types, gene enrichment analysis, publication-level figures, group interaction plotting, and result export in one Excel file for seamless sharing and communication.
Maintained by Yunze Liu. Last updated 2 months ago.
enrichment-analysisgeneid-converterplotting
0.5 match 56 stars 6.00 score 24 scripts 1 dependents
shanejorr
usincometaxes:Calculate Federal and State Income Taxes in the United States
Calculates federal and state income taxes in the United States. It acts as a wrapper to the NBER's TAXSIM 35 (<http://taxsim.nber.org/taxsim35/>) tax simulator. TAXSIM 35 conducts the calculations, while 'usincometaxes' prepares the data for TAXSIM 35, sends the data to TAXSIM 35's server or communicates with the Web Assembly file, retrieves the data, and places it into a data frame. All without the user worrying about this process.
Maintained by Shane Orr. Last updated 1 years ago.
0.5 match 13 stars 5.99 score 15 scriptscran
serial:The Serial Interface Package
Enables reading and writing binary and ASCII data to RS232/RS422/RS485 or any other virtual serial interface of the computer.
Maintained by Martin Seilmayer. Last updated 5 years ago.
1.9 match 1.48 score 1 dependents
novonordisk-opensource
zephyr:Structured Messages and Options
Provides a structured framework for consistent user communication and configuration management for package developers.
Maintained by Aksel Thomsen. Last updated 3 days ago.
0.6 match 2 stars 4.75 score 2 scripts
earowang
tsibbletalk:Interactive Graphics for Tsibble Objects
A shared tsibble data easily communicates between htmlwidgets on both client and server sides, powered by 'crosstalk'. A shiny module is provided to visually explore periodic/aperiodic temporal patterns.
Maintained by Earo Wang. Last updated 1 years ago.
0.5 match 28 stars 4.89 score 28 scripts
jorgetendeiro
GGUM:Generalized Graded Unfolding Model
An implementation of the generalized graded unfolding model (GGUM) in R, see Roberts, Donoghue, and Laughlin (2000) <doi:10.1177/01466216000241001>). It allows to simulate data sets based on the GGUM. It fits the GGUM and the GUM, and it retrieves item and person parameter estimates. Several plotting functions are available (item and test information functions; item and test characteristic curves; item category response curves). Additionally, there are some functions that facilitate the communication between R and 'GGUM2004'. Finally, a model-fit checking utility, MODFIT(), is also available.
Maintained by Jorge N. Tendeiro. Last updated 2 years ago.
0.5 match 6 stars 4.99 score 18 scripts 1 dependentsropensci
concstats:Market Structure, Concentration and Inequality Measures
Based on individual market shares of all participants in a market or space, the package offers a set of different structural and concentration measures frequently - and not so frequently - used in research and in practice. Measures can be calculated in groups or individually. The calculated measure or the resulting vector in table format should help practitioners make more informed decisions. Methods used in this package are from: 1. Chang, E. J., Guerra, S. M., de Souza Penaloza, R. A. & Tabak, B. M. (2005) "Banking concentration: the Brazilian case". 2. Cobham, A. and A. Summer (2013). "Is It All About the Tails? The Palma Measure of Income Inequality". 3. Garcia Alba Idunate, P. (1994). "Un Indice de dominancia para el analisis de la estructura de los mercados". 4. Ginevicius, R. and S. Cirba (2009). "Additive measurement of market concentration" <doi:10.3846/1611-1699.2009.10.191-198>. 5. Herfindahl, O. C. (1950), "Concentration in the steel industry" (PhD thesis). 6. Hirschmann, A. O. (1945), "National power and structure of foreign trade". 7. Melnik, A., O. Shy, and R. Stenbacka (2008), "Assessing market dominance" <doi:10.1016/j.jebo.2008.03.010>. 8. Palma, J. G. (2006). "Globalizing Inequality: 'Centrifugal' and 'Centripetal' Forces at Work". 9. Shannon, C. E. (1948). "A Mathematical Theory of Communication". 10. Simpson, E. H. (1949). "Measurement of Diversity" <doi:10.1038/163688a0>.
Maintained by Andreas Schneider. Last updated 1 years ago.
business-analyticscompetitionconcentrationdiversityinequalitypackage-development
0.5 match 7 stars 5.02 score 15 scriptspachadotdev
cpp11eigen:An 'Eigen' Interface
Provides function declarations and inline function definitions that facilitate communication between R and the 'Eigen' 'C++' library for linear algebra and scientific computing.
Maintained by Mauricio Vargas Sepulveda. Last updated 5 months ago.
cppcpp11eigenhacktoberfestlinear-algebra
0.5 match 2 stars 4.60 score 1 scripts
gagolews
stringx:Replacements for Base String Functions Powered by 'stringi'
English is the native language for only 5% of the World population. Also, only 17% of us can understand this text. Moreover, the Latin alphabet is the main one for merely 36% of the total. The early computer era, now a very long time ago, was dominated by the US. Due to the proliferation of the internet, smartphones, social media, and other technologies and communication platforms, this is no longer the case. This package replaces base R string functions (such as grep(), tolower(), sprintf(), and strptime()) with ones that fully support the Unicode standards related to natural language and date-time processing. It also fixes some long-standing inconsistencies, and introduces some new, useful features. Thanks to 'ICU' (International Components for Unicode) and 'stringi', they are fast, reliable, and portable across different platforms.
Maintained by Marek Gagolewski. Last updated 2 months ago.
icuicu4cnatural-language-processingnlpregexregexpstring-manipulationstringitexttext-processingunicode
0.5 match 28 stars 4.75 score 1 scripts
bioc
fgga:Hierarchical ensemble method based on factor graph
Package that implements the FGGA algorithm. This package provides a hierarchical ensemble method based ob factor graphs for the consistent cross-ontology annotation of protein coding genes. FGGA embodies elements of predicate logic, communication theory, supervised learning and inference in graphical models.
Maintained by Flavio Spetale. Last updated 5 months ago.
softwarestatisticalmethodclassificationnetworknetworkinferencesupportvectormachinegraphandnetworkgo
0.5 match 3 stars 4.48 score 6 scriptsbioc
BiocBook:Write, containerize, publish and version Quarto books with Bioconductor
A BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, ...) who wish to 1) write (compile a body of biological and/or bioinformatics knowledge), 2) containerize (provide Docker images to reproduce the examples illustrated in the compendium), 3) publish (deploy an online book to disseminate the compendium), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases).
Maintained by Jacques Serizay. Last updated 5 months ago.
infrastructurereportwritingsoftware
0.5 match 3 stars 4.48 score 4 scripts
stephen-amori
apmx:Automated Population Pharmacokinetic Dataset Assembly
Automated methods to assemble population PK (pharmacokinetic) and PKPD (pharmacodynamic) datasets for analysis in 'NONMEM' (non-linear mixed effects modeling) by Bauer (2019) <doi:10.1002/psp4.12404>. The package includes functions to build datasets from SDTM (study data tabulation module) <https://www.cdisc.org/standards/foundational/sdtm>, ADaM (analysis dataset module) <https://www.cdisc.org/standards/foundational/adam>, or other dataset formats. The package will combine population datasets, add covariates, and create documentation to support regulatory submission and internal communication.
Maintained by Stephen Amori. Last updated 1 years ago.
0.5 match 5 stars 4.40 score 10 scripts
rosawojciech
bigchess:Read, Write, Manipulate, Explore Chess PGN Files and R API to UCI Chess Engines
Provides functions for reading *.PGN files with more than one game, including large files without copying it into RAM (using 'ff' package or 'RSQLite' package). Handle chess data and chess aggregated data, count figure moves statistics, create player profile, plot winning chances, browse openings. Set of functions of R API to communicate with UCI-protocol based chess engines.
Maintained by Wojciech Rosa. Last updated 4 years ago.
0.5 match 10 stars 4.29 score 39 scripts
taridwong
CTTvis:Visualize Item Metrics of the Classical Test Theory Framework
Visualizes results of item analysis such as item difficulty, item discrimination, and coefficient alpha for ease of result communication.
Maintained by Tarid Wongvorachan. Last updated 3 months ago.
0.5 match 4.00 scorebioc
easier:Estimate Systems Immune Response from RNA-seq data
This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input. We integrate RNA-seq data with different types of prior knowledge to extract quantitative descriptors of the tumor microenvironment from several points of view, including composition of the immune repertoire, and activity of intra- and extra-cellular communications. Then, we use multi-task machine learning trained in TCGA data to identify how these descriptors can simultaneously predict several state-of-the-art hallmarks of anti-cancer immune response. In this way we derive cancer-specific models and identify cancer-specific systems biomarkers of immune response. These biomarkers have been experimentally validated in the literature and the performance of EaSIeR predictions has been validated using independent datasets form four different cancer types with patients treated with anti-PD1 or anti-PDL1 therapy.
Maintained by Oscar Lapuente-Santana. Last updated 5 months ago.
geneexpressionsoftwaretranscriptionsystemsbiologypathwaysgenesetenrichmentimmunooncologyepigeneticsclassificationbiomedicalinformaticsregressionexperimenthubsoftware
0.5 match 4.20 score 16 scripts
posit-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.
0.5 match 4 stars 4.00 score 1 scripts
marcinkosinski
RZabbix:R Module for Working with the 'Zabbix API'
R interface to the 'Zabbix API' data <https://www.zabbix.com/documentation/3.0/manual/api/reference>. Enables easy and direct communication with 'Zabbix API' from 'R'.
Maintained by Marcin Kosinski. Last updated 8 years ago.
0.5 match 12 stars 3.78 score 3 scripts
krisanata
animbook:Visualizing Changes in Performance Measures and Demographic Affiliations using Animation
Create an interactive visualization to be used for communication purposes. Providing the function for preparing, plotting, and animating the data. Krisanat Anukarnsakulchularp (2023) <https://github.com/KrisanatA/animbook-journal>
Maintained by Krisanat Anukarnsakulchularp. Last updated 11 months ago.
0.5 match 1 stars 3.70 score 10 scripts
alaninglis
corrViz:Visualise Correlations
An investigative tool designed to help users visualize correlations between variables in their datasets. This package aims to provide an easy and effective way to explore and visualize these correlations, making it easier to interpret and communicate results.
Maintained by Alan Inglis. Last updated 1 years ago.
0.5 match 1 stars 3.70 score 4 scripts
onofriandreapg
statforbiology:Data Analyses in Agriculture and Biology
Contains several tools for nonlinear regression analyses and general data analysis in biology and agriculture. Contains also datasets for practicing and teaching purposes. Supports the blog: Onofri (2024) "Fixing the bridge between biologists and statisticians" <https://www.statforbiology.com> and the book: Onofri (2024) "Experimental Methods in Agriculture" <https://www.statforbiology.com/_statbookeng/>. The blog is a collection of short articles aimed at improving the efficiency of communication between biologists and statisticians, as pointed out in Kozak (2016) <doi:10.1590/0103-9016-2015-0399>, spreading a better awareness of the potential usefulness, beauty and limitations of biostatistic.
Maintained by Andrea Onofri. Last updated 4 months ago.
0.5 match 1 stars 3.40 score
tonyfischetti
libbib:Various Utilities for Library Science/Assessment and Cataloging
Provides functions for validating and normalizing bibliographic codes such as ISBN, ISSN, and LCCN. Also includes functions to communicate with the WorldCat API, translate Call numbers (Library of Congress and Dewey Decimal) to their subject classifications or subclassifications, and provides various loadable data files such call number / subject crosswalks and code tables.
Maintained by Tony Fischetti. Last updated 2 years ago.
0.5 match 3.20 score 32 scripts
david-hammond
piecenorms:Calculate a Piecewise Normalised Score Using Class Intervals
Provides an implementation of piecewise normalisation techniques useful when dealing with the communication of skewed and highly skewed data. It also provides utilities that recommends a normalisation technique based on the distribution of the data.
Maintained by David Hammond. Last updated 8 months ago.
0.5 match 1 stars 3.00 score 3 scripts
tidy-intelligence
uisapi:Access the UNESCO Institute for Statistics API
Retrieve data from the UNESCO Institute for Statistics (UIS) API <https://api.uis.unesco.org/api/public/documentation/>. UIS provides public access to more than 4,000 indicators focusing on education, science and technology, culture, and communication.
Maintained by Christoph Scheuch. Last updated 10 days ago.
0.5 match 1 stars 3.00 scorecran
XR:A Structure for Interfaces from R
Support for interfaces from R to other languages, built around a class for evaluators and a combination of functions, classes and methods for communication. Will be used through a specific language interface package. Described in the book "Extending R".
Maintained by John Chambers. Last updated 7 years ago.
0.5 match 2.95 score 3 dependents
aquincum
Rexperigen:R Interface to Experigen
Provides convenience functions to communicate with an Experigen server: Experigen (<http://github.com/aquincum/experigen>) is an online framework for creating linguistic experiments, and it stores the results on a dedicated server. This package can be used to retrieve the results from the server, and it is especially helpful with registered experiments, as authentication with the server has to happen.
Maintained by Daniel Szeredi. Last updated 9 years ago.
0.5 match 1 stars 2.95 score 18 scripts
allenday
Storm:Write Storm Bolts in R using the Storm Multi-Language Protocol.
Storm is a distributed real-time computation system. Similar to how Hadoop provides a set of general primitives for doing batch processing, Storm provides a set of general primitives for doing real-time computation. . Storm includes a "Multi-Language" (or "Multilang") Protocol to allow implementation of Bolts and Spouts in languages other than Java. This R extension provides implementations of utility functions to allow an application developer to focus on application-specific functionality rather than Storm/R communications plumbing.
Maintained by Allen Day. Last updated 10 years ago.
0.5 match 2.00 score 6 scripts
aljgutier
rwfec:R Wireless, Forward Error Correction
Communications simulation package supporting forward error correction.
Maintained by Alberto Gutierrez. Last updated 9 years ago.
0.6 match 1.70 score 3 scriptscran
gp:Maximum Likelihood Estimation of the Generalized Poisson Distribution
Functions to estimate the parameters of the generalized Poisson distribution with or without covariates using maximum likelihood. The references include Nikoloulopoulos A.K. & Karlis D. (2008). "On modeling count data: a comparison of some well-known discrete distributions". Journal of Statistical Computation and Simulation, 78(3): 437--457, <doi:10.1080/10629360601010760> and Consul P.C. & Famoye F. (1992). "Generalized Poisson regression model". Communications in Statistics - Theory and Methods, 21(1): 89--109, <doi:10.1080/03610929208830766>.
Maintained by Michail Tsagris. Last updated 1 years ago.
0.5 match 1.78 score 2 dependents
princethewinner
FiRE:Finder of Rare Entities (FiRE)
The algorithm assigns rareness/ outlierness score to every sample in voluminous datasets. The algorithm makes multiple estimations of the proximity between a pair of samples, in low-dimensional spaces. To compute proximity, FiRE uses Sketching, a variant of locality sensitive hashing. For more details: Jindal, A., Gupta, P., Jayadeva and Sengupta, D., 2018. Discovery of rare cells from voluminous single cell expression data. Nature Communications, 9(1), p.4719. <doi:10.1038/s41467-018-07234-6>.
Maintained by Prashant Gupta. Last updated 4 years ago.
0.5 match 1.30 score 7 scriptscran
bender:Bender Client
R client for Bender Hyperparameters optimizer : <https://bender.dreem.com> The R client allows you to communicate with the Bender API and therefore submit some new trials within your R script itself.
Maintained by Valentin Thorey. Last updated 6 years ago.
0.5 match 1.00 score 1 scripts
gianluca-sottile
changepointsVar:Change-Points Detections for Changes in Variance
Detection of change-points for variance of heteroscedastic Gaussian variables with piecewise constant variance function. Adelfio, G. (2012), Change-point detection for variance piecewise constant models, Communications in Statistics, Simulation and Computation, 41:4, 437-448, <doi:10.1080/03610918.2011.592248>.
Maintained by Gianluca Sottile. Last updated 1 years ago.
0.5 match 1.00 score 4 scriptscran
BHAI:Estimate the Burden of Healthcare-Associated Infections
Provides an approach which is based on the methodology of the Burden of Communicable Diseases in Europe (BCoDE) and can be used for large and small samples such as individual countries. The Burden of Healthcare-Associated Infections (BHAI) is estimated in disability-adjusted life years, number of infections as well as number of deaths per year. Results can be visualized with various plotting functions and exported into tables.
Maintained by Benedikt Zacher. Last updated 5 years ago.
0.5 match 1.00 score
mubarakfadhlul
PODES:Village Potential Statistics of Indonesia
Village potential statistics (PODES) collects various information on village potential and challenges faced by villages in Indonesia. Information related to village potential includes economy, security, health, employment, communication and information, sports, entertainment, development, community empowerment, education, socio-culture, transportation in the village. Information related to challenges includes natural disasters, public health, environmental pollution, social problems and security disturbances that occur in the village.
Maintained by Fadhlul Mubarak. Last updated 4 months ago.
0.5 match 1.00 score
audreyqyfu
cancerGI:Analyses of Cancer Gene Interaction
Functions to perform the following analyses: i) inferring epistasis from RNAi double knockdown data; ii) identifying gene pairs of multiple mutation patterns; iii) assessing association between gene pairs and survival; and iv) calculating the smallworldness of a graph (e.g., a gene interaction network). Data and analyses are described in Wang, X., Fu, A. Q., McNerney, M. and White, K. P. (2014). Widespread genetic epistasis among breast cancer genes. Nature Communications. 5 4828. <doi:10.1038/ncomms5828>.
Maintained by Audrey Q. Fu. Last updated 2 years ago.
0.5 match 1.00 scorecran
fsn:Rosenthal's Fail Safe Number and Related Functions
Estimation of Rosenthal's fail safe number including confidence intervals. The relevant papers are the following. Konstantinos C. Fragkos, Michail Tsagris and Christos C. Frangos (2014). "Publication Bias in Meta-Analysis: Confidence Intervals for Rosenthal's Fail-Safe Number". International Scholarly Research Notices, Volume 2014. <doi:10.1155/2014/825383>. Konstantinos C. Fragkos, Michail Tsagris and Christos C. Frangos (2017). "Exploring the distribution for the estimator of Rosenthal's fail-safe number of unpublished studies in meta-analysis". Communications in Statistics-Theory and Methods, 46(11):5672--5684. <doi:10.1080/03610926.2015.1109664>.
Maintained by Michail Tsagris. Last updated 3 months ago.
0.5 match 1.00 score
