Showing 39 of total 39 results (show query)
rstudio
promises:Abstractions for Promise-Based Asynchronous Programming
Provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to 'JavaScript' promises, but with a syntax that is idiomatic R.
Maintained by Joe Cheng. Last updated 1 months ago.
115.6 match 204 stars 17.10 score 688 scripts 2.6k dependents
bioc
PROMISE:PRojection Onto the Most Interesting Statistical Evidence
A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019
Maintained by Stan Pounds. Last updated 5 months ago.
microarrayonechannelmultiplecomparisongeneexpression
63.1 match 5.44 score 46 scripts 1 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 20 hours ago.
asyncasynchronous-tasksconcurrencydistributed-computinghigh-performance-computingparallel-computing
14.4 match 217 stars 11.94 score 130 scripts 7 dependents
r-lib
coro:'Coroutines' for R
Provides 'coroutines' for R, a family of functions that can be suspended and resumed later on. This includes 'async' functions (which await) and generators (which yield). 'Async' functions are based on the concurrency framework of the 'promises' package. Generators are based on a dependency free iteration protocol defined in 'coro' and are compatible with iterators from the 'reticulate' package.
Maintained by Lionel Henry. Last updated 19 days ago.
asynccoroutinesgeneratoriteratorpromisesreticulate
10.5 match 166 stars 11.88 score 105 scripts 50 dependents
hadley
pryr:Tools for Computing on the Language
Useful tools to pry back the covers of R and understand the language at a deeper level.
Maintained by Hadley Wickham. Last updated 1 years ago.
7.9 match 204 stars 11.85 score 1.9k scripts 56 dependents
wlandau
crew:A Distributed Worker Launcher Framework
In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'NNG'-powered 'mirai' R package by Gao (2023) <doi:10.5281/zenodo.7912722> is a sleek and sophisticated scheduler that efficiently processes these intense workloads. The 'crew' package extends 'mirai' with a unifying interface for third-party worker launchers. Inspiration also comes from packages. 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischel, and Surmann (2017) <doi:10.21105/joss.00135>.
Maintained by William Michael Landau. Last updated 12 hours ago.
6.3 match 136 stars 11.19 score 243 scripts 2 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 12 hours ago.
concurrencyhttpsipc-messagemessaging-librarynngrpcsocket-communicationsynchronization-primitivestcp-protocolwebsocketmbedtls
5.5 match 60 stars 9.81 score 28 scripts 9 dependentshadley
lazyeval:Lazy (Non-Standard) Evaluation
An alternative approach to non-standard evaluation using formulas. Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.
Maintained by Hadley Wickham. Last updated 3 years ago.
3.3 match 131 stars 15.74 score 520 scripts 1.8k dependentsrstudio
chromote:Headless Chrome Web Browser Interface
An implementation of the 'Chrome DevTools Protocol', for controlling a headless Chrome web browser.
Maintained by Winston Chang. Last updated 1 days ago.
3.0 match 164 stars 13.82 score 162 scripts 28 dependents
jeroen
V8:Embedded JavaScript and WebAssembly Engine for R
An R interface to V8 <https://v8.dev>: Google's open source JavaScript and WebAssembly engine. This package can be compiled either with V8 version 6 and up or NodeJS when built as a shared library.
Maintained by Jeroen Ooms. Last updated 9 hours ago.
2.0 match 201 stars 15.80 score 508 scripts 336 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 7 days ago.
1.8 match 246 stars 17.66 score 1.9k scripts 1.1k dependents
cmmr
jobqueue:Run Interruptible Code Asynchronously
Takes an R expression and returns a Job object with a $stop() method which can be called to terminate the background job. Also provides timeouts and other mechanisms for automatically terminating a background job. The result of the expression is available synchronously via $result or asynchronously with callbacks or through the 'promises' package framework.
Maintained by Daniel P. Smith. Last updated 15 days ago.
5.0 match 2 stars 5.89 score 12 scriptsbioc
CCPROMISE:PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data
Perform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with multiple endpoints. A probe level analysis is also implemented.
Maintained by Xueyuan Cao. Last updated 5 months ago.
7.9 match 3.30 score 1 scripts
qsbase
qs:Quick Serialization of R Objects
Provides functions for quickly writing and reading any R object to and from disk.
Maintained by Travers Ching. Last updated 8 days ago.
compressiondata-storageencodingserializationlibzstdlz4cpp
1.9 match 414 stars 13.91 score 2.5k scripts 51 dependents
schochastics
networkdata:Repository of Network Datasets
The package contains a large collection of network dataset with different context. This includes social networks, animal networks and movie networks. All datasets are in 'igraph' format.
Maintained by David Schoch. Last updated 12 months ago.
4.5 match 143 stars 5.01 score 143 scripts
lawremi
rsolr:R to Solr Interface
A comprehensive R API for querying Apache Solr databases. A Solr core is represented as a data frame or list that supports Solr-side filtering, sorting, transformation and aggregation, all through the familiar base R API. Queries are processed lazily, i.e., a query is only sent to the database when the data are required.
Maintained by Michael Lawrence. Last updated 3 years ago.
6.0 match 9 stars 3.65 score 6 scripts
justincally
VicmapR:Access Victorian Spatial Data Through Web File Services (WFS)
Easily interfaces R to spatial datasets available through the Victorian Government's WFS (Web Feature Service): <https://opendata.maps.vic.gov.au/geoserver/ows?request=GetCapabilities&service=wfs>, which allows users to read in 'sf' data from these sources. VicmapR uses the lazy querying approach and code developed by Teucher et al. (2021) for the 'bcdata' R package <doi:10.21105/joss.02927>.
Maintained by Justin Cally. Last updated 6 months ago.
3.4 match 17 stars 6.14 score 18 scriptsbioc
IgGeneUsage:Differential gene usage in immune repertoires
Detection of biases in the usage of immunoglobulin (Ig) genes is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage between biological conditions using a probabilistic model which is analyzed computationally by Bayes inference. With this IgGeneUsage also avoids some common problems related to the current practice of null-hypothesis significance testing.
Maintained by Simo Kitanovski. Last updated 5 months ago.
differentialexpressionregressiongeneticsbayesianbiomedicalinformaticsimmunooncologymathematicalbiologyb-cell-receptorbcr-repertoiredifferential-analysisdifferential-gene-expressionhigh-throughput-sequencingimmune-repertoireimmune-repertoire-analysisimmune-repertoiresimmunogenomicsimmunoglobulinimmunoinformaticsimmunological-bioinformaticsimmunologytcr-repertoirevdj-recombinationcpp
2.8 match 6 stars 5.92 score 1 scripts
vsimko
rroad:Road Condition Analysis
Computation of the International Roughness Index (IRI) given a longitudinal road profile. The IRI can be calculated for a single road segment or for a sequence of segments with a fixed length (e. g. 100m). For the latter, an overlap of the segments can be selected. The IRI and likewise the algorithms for its determination are defined in Sayers, Michael W; Gillespie, Thomas D; Queiroz, Cesar A.V. 1986. The International Road Roughness Experiment (IRRE) : establishing correlation and a calibration standard for measurements. World Bank technical paper; no. WTP 45. Washington, DC : The World Bank. (ISBN 0-8213-0589-1) available from <http://documents.worldbank.org/curated/en/326081468740204115>.
Maintained by Viliam Simko. Last updated 5 years ago.
carindexirimonitoringroad-conditionroad-safetyroad-trafficroadsroads-and-highwaysroughness
3.4 match 13 stars 4.11 score 7 scripts
dipterix
dipsaus:A Dipping Sauce for Data Analysis and Visualizations
Works as an "add-on" to packages like 'shiny', 'future', as well as 'rlang', and provides utility functions. Just like dipping sauce adding flavors to potato chips or pita bread, 'dipsaus' for data analysis and visualizations adds handy functions and enhancements to popular packages. The goal is to provide simple solutions that are frequently asked for online, such as how to synchronize 'shiny' inputs without freezing the app, or how to get memory size on 'Linux' or 'MacOS' system. The enhancements roughly fall into these four categories: 1. 'shiny' input widgets; 2. high-performance computing using the 'future' package; 3. modify R calls and convert among numbers, strings, and other objects. 4. utility functions to get system information such like CPU chip-set, memory limit, etc.
Maintained by Zhengjia Wang. Last updated 4 days ago.
1.8 match 13 stars 7.90 score 85 scripts 3 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.
3.6 match 2.28 score 38 scripts
robitalec
ScaleInMultilayerNetworks:Package Accompanying: The Problem And Promise Of Scale In Multilayer Animal Social Networks.
Scale remains a foundational concept in ecology. Spatial scale, for instance, has become a central consideration in the way we understand landscape ecology and animal space use. Meanwhile, scale-dependent social processes can range from fine-scale interactions to co-occurrence and overlapping home ranges. Furthermore, sociality can vary within and across seasons. Multilayer networks promise the explicit integration of the social, spatial and, temporal contexts. Given the complex interplay of sociality and animal space use in heterogeneous landscapes, there remains an important gap in our understanding of the influence of scale on animal social networks. Using an empirical case study, we discuss ways of considering social, spatial and, temporal scale in the context of multilayer caribou social networks. Effective integration of social and spatial processes, including biologically meaningful scales, within the context of animal social networks is an emerging area of research. We incorporate perspectives that link the social environment to spatial processes across scales in a multilayer context.
Maintained by Alec L. Robitaille. Last updated 4 years ago.
ecologymultilayer-networkssocial-network-analysis
3.3 match 1 stars 2.00 score
pik-piam
madrat:May All Data be Reproducible and Transparent (MADRaT) *
Provides a framework which should improve reproducibility and transparency in data processing. It provides functionality such as automatic meta data creation and management, rudimentary quality management, data caching, work-flow management and data aggregation. * The title is a wish not a promise. By no means we expect this package to deliver everything what is needed to achieve full reproducibility and transparency, but we believe that it supports efforts in this direction.
Maintained by Jan Philipp Dietrich. Last updated 17 hours ago.
0.5 match 15 stars 11.01 score 83 scripts 38 dependents
bioc
runibic:runibic: row-based biclustering algorithm for analysis of gene expression data in R
This package implements UbiBic algorithm in R. This biclustering algorithm for analysis of gene expression data was introduced by Zhenjia Wang et al. in 2016. It is currently considered the most promising biclustering method for identification of meaningful structures in complex and noisy data.
Maintained by Patryk Orzechowski. Last updated 5 months ago.
microarrayclusteringgeneexpressionsequencingcoveragecppopenmp
0.5 match 4 stars 5.20 score 7 scripts
mabelc
ssc:Semi-Supervised Classification Methods
Provides a collection of self-labeled techniques for semi-supervised classification. In semi-supervised classification, both labeled and unlabeled data are used to train a classifier. This learning paradigm has obtained promising results, specifically in the presence of a reduced set of labeled examples. This package implements a collection of self-labeled techniques to construct a classification model. This family of techniques enlarges the original labeled set using the most confident predictions to classify unlabeled data. The techniques implemented can be applied to classification problems in several domains by the specification of a supervised base classifier. At low ratios of labeled data, it can be shown to perform better than classical supervised classifiers.
Maintained by Christoph Bergmeir. Last updated 5 years ago.
0.5 match 9 stars 5.22 score 62 scripts 1 dependents
billvenables
lazyData:A LazyData Facility
Supplies a LazyData facility for packages which have data sets but do not provide LazyData: true. A single function is is included, requireData, which is a drop-in replacement for base::require, but carrying the additional functionality. By default, it suppresses package startup messages as well. See argument 'reallyQuitely'.
Maintained by Bill Venables. Last updated 8 years ago.
1.7 match 1.48 score 2 scripts 1 dependents
p-rocha
SoundShape:Sound Waves Onto Morphometric Data
Implement a promising, and yet little explored protocol for bioacoustical analysis, the eigensound method by MacLeod, Krieger and Jones (2013) <doi:10.4404/hystrix-24.1-6299>. Eigensound is a multidisciplinary method focused on the direct comparison between stereotyped sounds from different species. 'SoundShape', in turn, provide the tools required for anyone to go from sound waves to Principal Components Analysis, using tools extracted from traditional bioacoustics (i.e. 'tuneR' and 'seewave' packages), geometric morphometrics (i.e. 'geomorph' package) and multivariate analysis (e.g. 'stats' package). For more information, please see Rocha and Romano (2021) and check 'SoundShape' repository on GitHub for news and updates <https://github.com/p-rocha/SoundShape>.
Maintained by Pedro Rocha. Last updated 5 months ago.
0.5 match 9 stars 4.73 score 12 scriptsbioc
cageminer:Candidate Gene Miner
This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments.
Maintained by Fabrício Almeida-Silva. Last updated 5 months ago.
softwaresnpfunctionalpredictiongenomewideassociationgeneexpressionnetworkenrichmentvariantannotationfunctionalgenomicsnetwork
0.5 match 1 stars 4.30 score 5 scripts
marcodvisser
aprof:Amdahl's Profiler, Directed Optimization Made Easy
Assists the evaluation of whether and where to focus code optimization, using Amdahl's law and visual aids based on line profiling. Amdahl's profiler organizes profiling output files (including memory profiling) in a visually appealing way. It is meant to help to balance development vs. execution time by helping to identify the most promising sections of code to optimize and projecting potential gains. The package is an addition to R's standard profiling tools and is not a wrapper for them.
Maintained by Marco D. Visser. Last updated 28 days ago.
0.5 match 21 stars 4.02 score 8 scripts
mightymetrika
holi:Higher Order Likelihood Inference Web Applications
Higher order likelihood inference is a promising approach for analyzing small sample size data. The 'holi' package provides web applications for higher order likelihood inference. It currently supports linear, logistic, and Poisson generalized linear models through the rstar_glm() function, based on Pierce and Bellio (2017) <doi:10.1111/insr.12232> and 'likelihoodAsy'. The package offers two main features: LA_rstar(), which launches an interactive 'shiny' application allowing users to fit models with rstar_glm() through their web browser, and sim_rstar_glm_pgsql(), which streamlines the process of launching a web-based 'shiny' simulation application that saves results to a user-created 'PostgreSQL' database.
Maintained by Mackson Ncube. Last updated 6 months ago.
0.5 match 3.48 score 5 scripts
czhong9106
SAME:Seamless Adaptive Multi-Arm Multi-Stage Enrichment
Design a Bayesian seamless multi-arm biomarker-enriched phase II/III design with the survival endpoint with allowing sample size re-estimation. James M S Wason, Jean E Abraham, Richard D Baird, Ioannis Gournaris, Anne-Laure Vallier, James D Brenton, Helena M Earl, Adrian P Mander (2015) <doi:10.1038/bjc.2015.278>. Guosheng Yin, Nan Chen, J. Jack Lee (2018) <doi:10.1007/s12561-017-9199-7>. Ying Yuan, Beibei Guo, Mark Munsell, Karen Lu, Amir Jazaeri (2016) <doi:10.1002/sim.6971>.
Maintained by Chengxue Zhong. Last updated 2 years ago.
1.7 match 1.00 score 1 scriptsmightymetrika
npboottprmFBar:Informative Nonparametric Bootstrap Test with Pooled Resampling
Sample sizes are often small due to hard to reach target populations, rare target events, time constraints, limited budgets, or ethical considerations. Two statistical methods with promising performance in small samples are the nonparametric bootstrap test with pooled resampling method, which is the focus of Dwivedi, Mallawaarachchi, and Alvarado (2017) <doi:10.1002/sim.7263>, and informative hypothesis testing, which is implemented in the 'restriktor' package. The 'npboottprmFBar' package uses the nonparametric bootstrap test with pooled resampling method to implement informative hypothesis testing. The bootFbar() function can be used to analyze data with this method and the persimon() function can be used to conduct performance simulations on type-one error and statistical power.
Maintained by Mackson Ncube. Last updated 6 months ago.
0.5 match 3.00 score 5 scripts
bioc
DeProViR:A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Protein-Protein Interactions
Emerging infectious diseases, exemplified by the zoonotic COVID-19 pandemic caused by SARS-CoV-2, are grave global threats. Understanding protein-protein interactions (PPIs) between host and viral proteins is essential for therapeutic targets and insights into pathogen replication and immune evasion. While experimental methods like yeast two-hybrid screening and mass spectrometry provide valuable insights, they are hindered by experimental noise and costs, yielding incomplete interaction maps. Computational models, notably DeProViR, predict PPIs from amino acid sequences, incorporating semantic information with GloVe embeddings. DeProViR employs a Siamese neural network, integrating convolutional and Bi-LSTM networks to enhance accuracy. It overcomes the limitations of feature engineering, offering an efficient means to predict host-virus interactions, which holds promise for antiviral therapies and advancing our understanding of infectious diseases.
Maintained by Matineh Rahmatbakhsh. Last updated 5 months ago.
proteomicssystemsbiologynetworkinferenceneuralnetworknetwork
0.5 match 1 stars 3.00 score 1 scripts
cran
OSTE:Optimal Survival Trees Ensemble
Function for growing survival trees ensemble ('Naz Gul', 'Nosheen Faiz', 'Dan Brawn', 'Rafal Kulakowski', 'Zardad Khan', and 'Berthold Lausen' (2020) <arXiv:2005.09043>) is given. The trees are grown by the method of random survival forest ('Marvin Wright', 'Andreas Ziegler' (2017) <doi:10.18637/jss.v077.i01>). The survival trees grown are assessed for both individual and collective performances. The ensemble can give promising results on fewer survival trees selected in the final ensemble.
Maintained by Naz Gul. Last updated 3 years ago.
0.5 match 1 stars 2.00 score
