Showing 87 of total 87 results (show query)
branchlab
metasnf:Meta Clustering with Similarity Network Fusion
Framework to facilitate patient subtyping with similarity network fusion and meta clustering. The similarity network fusion (SNF) algorithm was introduced by Wang et al. (2014) in <doi:10.1038/nmeth.2810>. SNF is a data integration approach that can transform high-dimensional and diverse data types into a single similarity network suitable for clustering with minimal loss of information from each initial data source. The meta clustering approach was introduced by Caruana et al. (2006) in <doi:10.1109/ICDM.2006.103>. Meta clustering involves generating a wide range of cluster solutions by adjusting clustering hyperparameters, then clustering the solutions themselves into a manageable number of qualitatively similar solutions, and finally characterizing representative solutions to find ones that are best for the user's specific context. This package provides a framework to easily transform multi-modal data into a wide range of similarity network fusion-derived cluster solutions as well as to visualize, characterize, and validate those solutions. Core package functionality includes easy customization of distance metrics, clustering algorithms, and SNF hyperparameters to generate diverse clustering solutions; calculation and plotting of associations between features, between patients, and between cluster solutions; and standard cluster validation approaches including resampled measures of cluster stability, standard metrics of cluster quality, and label propagation to evaluate generalizability in unseen data. Associated vignettes guide the user through using the package to identify patient subtypes while adhering to best practices for unsupervised learning.
Maintained by Prashanth S Velayudhan. Last updated 6 days ago.
bioinformaticsclusteringmetaclusteringsnf
85.3 match 8 stars 8.21 score 30 scripts
ropensci
webmockr:Stubbing and Setting Expectations on 'HTTP' Requests
Stubbing and setting expectations on 'HTTP' requests. Includes tools for stubbing 'HTTP' requests, including expected request conditions and response conditions. Match on 'HTTP' method, query parameters, request body, headers and more. Can be used for unit tests or outside of a testing context.
Maintained by Scott Chamberlain. Last updated 2 months ago.
httphttpsapiweb-servicescurlmockmockingfakewebhttp-mockingtestingtesting-toolstddhttp-mock
44.3 match 49 stars 8.29 score 141 scripts 1 dependentsropensci
vcr:Record 'HTTP' Calls to Disk
Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.
Maintained by Scott Chamberlain. Last updated 27 days ago.
httphttpsapiweb-servicescurlmockmockinghttp-mockingtestingtesting-toolstddunit-testingvcr
31.8 match 77 stars 10.06 score 165 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.
33.6 match 81 stars 9.46 score 276 scripts 1 dependentsropensci
crul:HTTP Client
A simple HTTP client, with tools for making HTTP requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>). The package name is a play on curl, the widely used command line tool for HTTP, and this package is built on top of the R package 'curl', an interface to 'libcurl' (<https://curl.se/libcurl/>).
Maintained by Scott Chamberlain. Last updated 8 months ago.
httphttpsapiweb-servicescurldownloadlibcurlasyncmockingcaching
17.3 match 107 stars 14.07 score 240 scripts 168 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 9 months ago.
24.6 match 33 stars 9.37 score 95 scripts 1 dependents
r-lib
mockery:Mocking Library for R
The two main functionalities of this package are creating mock objects (functions) and selectively intercepting calls to a given function that originate in some other function. It can be used with any testing framework available for R. Mock objects can be injected with either this package's own stub() function or a similar with_mock() facility present in the 'testthat' package.
Maintained by Hadley Wickham. Last updated 1 years ago.
17.8 match 100 stars 11.57 score 504 scripts 5 dependents
ohdsi
omock:Creation of Mock Observational Medical Outcomes Partnership Common Data Model
Creates mock data for testing and package development for the Observational Medical Outcomes Partnership common data model. The package offers functions crafted with pipeline-friendly implementation, enabling users to effortlessly include only the necessary tables for their testing needs.
Maintained by Mike Du. Last updated 2 months ago.
26.4 match 2 stars 7.44 score 45 scripts 1 dependents
krlmlr
mockr:Mocking in R
Provides a means to mock a package function, i.e., temporarily substitute it for testing. Designed as a drop-in replacement for the now deprecated 'testthat::with_mock()' and 'testthat::local_mock()'.
Maintained by Kirill Müller. Last updated 4 months ago.
14.7 match 18 stars 8.26 score 37 scripts
jthomasmock
gtExtras:Extending 'gt' for Beautiful HTML Tables
Provides additional functions for creating beautiful tables with 'gt'. The functions are generally wrappers around boilerplate or adding opinionated niche capabilities and helpers functions.
Maintained by Thomas Mock. Last updated 12 months ago.
data-sciencedata-visualizationdatascienceggplot2gtplotssparklinesparkline-graphssparklinestables
9.1 match 201 stars 11.66 score 2.4k scripts 5 dependents
bioc
splatter:Simple Simulation of Single-cell RNA Sequencing Data
Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.
Maintained by Luke Zappia. Last updated 4 months ago.
singlecellrnaseqtranscriptomicsgeneexpressionsequencingsoftwareimmunooncologybioconductorbioinformaticsscrna-seqsimulation
9.3 match 224 stars 9.92 score 424 scripts 1 dependents
jakubnowicki
fixtuRes:Mock Data Generator
Generate mock data in R using YAML configuration.
Maintained by Jakub Nowicki. Last updated 3 years ago.
fixturesmock-datamock-data-generatortest-data-generatoryaml-configuration
18.1 match 16 stars 4.98 score 12 scriptsr-lib
testthat:Unit Testing for R
Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy to learn and use, and integrates with your existing 'workflow'.
Maintained by Hadley Wickham. Last updated 1 months ago.
4.1 match 900 stars 20.99 score 74k scripts 471 dependentsropensci
restez:Create and Query a Local Copy of 'GenBank' in R
Download large sections of 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local SQL-based database. A user can then query this database using 'restez' functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez> wrappers.
Maintained by Joel H. Nitta. Last updated 25 days ago.
10.8 match 26 stars 7.01 score 175 scripts 1 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 12 months ago.
8.3 match 82 stars 8.04 score 49 scripts
tlverse
tmle3mopttx:Targeted Maximum Likelihood Estimation of the Mean under Optimal Individualized Treatment
This package estimates the optimal individualized treatment rule for the categorical treatment using Super Learner (sl3). In order to avoid nested cross-validation, it uses split-specific estimates of Q and g to estimate the rule as described by Coyle et al. In addition, it provides the Targeted Maximum Likelihood estimates of the mean performance using CV-TMLE under such estimated rules. This is an adapter package for use with the tmle3 framework and the tlverse software ecosystem for Targeted Learning.
Maintained by Ivana Malenica. Last updated 3 years ago.
categorical-treatmentcausal-inferenceheterogeneous-effectsmachine-learningoptimal-individualized-treatmenttargeted-learningvariable-importance
14.0 match 13 stars 4.28 score 49 scripts 1 dependents
usepa
tcpl:ToxCast Data Analysis Pipeline
The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.
Maintained by Jason Brown. Last updated 12 days ago.
6.3 match 36 stars 9.39 score 90 scripts
friendly
heplots:Visualizing Hypothesis Tests in Multivariate Linear Models
Provides HE plot and other functions for visualizing hypothesis tests in multivariate linear models. HE plots represent sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses (in two dimensions) and ellipsoids (in three dimensions). The related 'candisc' package provides visualizations in a reduced-rank canonical discriminant space when there are more than a few response variables.
Maintained by Michael Friendly. Last updated 8 days ago.
linear-hypothesesmatricesmultivariate-linear-modelsplotrepeated-measure-designsvisualizing-hypothesis-tests
4.6 match 9 stars 11.78 score 1.1k scripts 7 dependentsohdsi
OmopSketch:Characterise Tables of an OMOP Common Data Model Instance
Summarises key information in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Assess suitability to perform specific epidemiological studies and explore the different domains to obtain feasibility counts and trends.
Maintained by Cecilia Campanile. Last updated 16 days ago.
7.1 match 2 stars 7.47 score 16 scripts 1 dependents
eheinzen
elo:Ranking Teams by Elo Rating and Comparable Methods
A flexible framework for calculating Elo ratings and resulting rankings of any two-team-per-matchup system (chess, sports leagues, 'Go', etc.). This implementation is capable of evaluating a variety of matchups, Elo rating updates, and win probabilities, all based on the basic Elo rating system. It also includes methods to benchmark performance, including logistic regression and Markov chain models.
Maintained by Ethan Heinzen. Last updated 1 years ago.
eloelo-ratinglogistic-regressionmarkov-chainmarkov-modelrankingsports-analyticscpp
7.3 match 37 stars 7.05 score 153 scripts
mayoverse
arsenal:An Arsenal of 'R' Functions for Large-Scale Statistical Summaries
An Arsenal of 'R' functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in 'R' and 'RStudio' and which use formulas and versatile summary statistics for summary tables and models. The primary functions include tableby(), a Table-1-like summary of multiple variable types 'by' the levels of one or more categorical variables; paired(), a Table-1-like summary of multiple variable types paired across two time points; modelsum(), which performs simple model fits on one or more endpoints for many variables (univariate or adjusted for covariates); freqlist(), a powerful frequency table across many categorical variables; comparedf(), a function for comparing data.frames; and write2(), a function to output tables to a document.
Maintained by Ethan Heinzen. Last updated 8 months ago.
baseline-characteristicsdescriptive-statisticsmodelingpaired-comparisonsreportingstatisticstableone
3.8 match 225 stars 13.40 score 1.2k scripts 15 dependentsbioc
MBECS:Evaluation and correction of batch effects in microbiome data-sets
The Microbiome Batch Effect Correction Suite (MBECS) provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.
Maintained by Michael Olbrich. Last updated 5 months ago.
batcheffectmicrobiomereportwritingvisualizationnormalizationqualitycontrol
10.5 match 4 stars 4.60 score 4 scripts
mrc-ide
EpiEstim:Estimate Time Varying Reproduction Numbers from Epidemic Curves
Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.
Maintained by Anne Cori. Last updated 7 months ago.
3.8 match 95 stars 12.06 score 1.0k scripts 7 dependents
nbenn
mockthat:Function Mocking for Unit Testing
With the deprecation of mocking capabilities shipped with 'testthat' as of 'edition 3' it is left to third-party packages to replace this functionality, which in some test-scenarios is essential in order to run unit tests in limited environments (such as no Internet connection). Mocking in this setting means temporarily substituting a function with a stub that acts in some sense like the original function (for example by serving a HTTP response that has been cached as a file). The only exported function 'with_mock()' is modeled after the eponymous 'testthat' function with the intention of providing a drop-in replacement.
Maintained by Nicolas Bennett. Last updated 2 years ago.
11.2 match 15 stars 3.94 score 5 scripts
ericmarcon
divent:Entropy Partitioning to Measure Diversity
Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>. 'divent' provides functions to estimate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.
Maintained by Eric Marcon. Last updated 3 days ago.
9.0 match 1 stars 4.81 score 1 scripts
darwin-eu
CodelistGenerator:Identify Relevant Clinical Codes and Evaluate Their Use
Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Maintained by Edward Burn. Last updated 4 days ago.
4.3 match 14 stars 9.94 score 165 scripts 4 dependents
rstudio
shiny:Web Application Framework for R
Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.
Maintained by Winston Chang. Last updated 6 days ago.
reactiverstudioshinyweb-appweb-development
2.0 match 5.5k stars 21.31 score 108k scripts 1.8k dependents
zeileis
betareg:Beta Regression
Beta regression for modeling beta-distributed dependent variables on the open unit interval (0, 1), e.g., rates and proportions, see Cribari-Neto and Zeileis (2010) <doi:10.18637/jss.v034.i02>. Moreover, extended-support beta regression models can accommodate dependent variables with boundary observations at 0 and/or 1. For the classical beta regression model, alternative specifications are provided: Bias-corrected and bias-reduced estimation, finite mixture models, and recursive partitioning for beta regression, see Grün, Kosmidis, and Zeileis (2012) <doi:10.18637/jss.v048.i11>.
Maintained by Achim Zeileis. Last updated 13 days ago.
3.8 match 10.63 score 904 scripts 22 dependents
merck
metalite.ae:Adverse Events Analysis Using 'metalite'
Analyzes adverse events in clinical trials using the 'metalite' data structure. The package simplifies the workflow to create production-ready tables, listings, and figures discussed in the adverse events analysis chapters of "R for Clinical Study Reports and Submission" by Zhang et al. (2022) <https://r4csr.org/>.
Maintained by Yujie Zhao. Last updated 2 months ago.
4.0 match 18 stars 9.45 score 31 scripts 2 dependentsdarwin-eu
PatientProfiles:Identify Characteristics of Patients in the OMOP Common Data Model
Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Maintained by Marti Catala. Last updated 25 days ago.
3.8 match 1 stars 9.97 score 225 scripts 9 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 4 days ago.
2.0 match 246 stars 17.64 score 1.9k scripts 1.1k dependentsbioc
DNABarcodes:A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode.
Maintained by Tilo Buschmann. Last updated 5 months ago.
preprocessingsequencingcppopenmp
7.5 match 4.51 score 27 scripts
rubenarslan
codebook:Automatic Codebooks from Metadata Encoded in Dataset Attributes
Easily automate the following tasks to describe data frames: Summarise the distributions, and labelled missings of variables graphically and using descriptive statistics. For surveys, compute and summarise reliabilities (internal consistencies, retest, multilevel) for psychological scales. Combine this information with metadata (such as item labels and labelled values) that is derived from R attributes. To do so, the package relies on 'rmarkdown' partials, so you can generate HTML, PDF, and Word documents. Codebooks are also available as tables (CSV, Excel, etc.) and in JSON-LD, so that search engines can find your data and index the metadata. The metadata are also available at your fingertips via RStudio Addins.
Maintained by Ruben Arslan. Last updated 3 months ago.
codebookdocumentationformrjson-ldmetadataspsswebapp
4.0 match 143 stars 8.29 score 229 scripts
georgekoliopanos
modgo:MOck Data GeneratiOn
Generation of mock data from a real dataset using rank normal inverse transformation.
Maintained by George Koliopanos. Last updated 9 months ago.
7.9 match 1 stars 4.00 score 3 scriptsbioc
ClustIRR:Clustering of immune receptor repertoires
ClustIRR analyzes repertoires of B- and T-cell receptors. It starts by identifying communities of immune receptors with similar specificities, based on the sequences of their complementarity-determining regions (CDRs). Next, it employs a Bayesian probabilistic models to quantify differential community occupancy (DCO) between repertoires, allowing the identification of expanding or contracting communities in response to e.g. infection or cancer treatment.
Maintained by Simo Kitanovski. Last updated 1 months ago.
clusteringimmunooncologysinglecellsoftwareclassificationb-cell-receptorbioinformaticsimmunoinformaticsimmunologyquantitative-methodsrep-seqrepertoire-analysist-cell-receptorcpp
5.3 match 2 stars 5.89 score 2 scriptsohdsi
CohortConstructor:Build and Manipulate Study Cohorts Using a Common Data Model
Create and manipulate study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model.
Maintained by Edward Burn. Last updated 8 hours ago.
3.1 match 2 stars 9.74 score 207 scripts 2 dependents
gsk-biostatistics
tfrmt:Applies Display Metadata to Analysis Results Datasets
Creates a framework to store and apply display metadata to Analysis Results Datasets (ARDs). The use of 'tfrmt' allows users to define table format and styling without the data, and later apply the format to the data.
Maintained by Becca Krouse. Last updated 4 months ago.
3.7 match 73 stars 8.03 score 84 scripts 1 dependents
ddalthorp
GenEst:Generalized Mortality Estimator
Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Maintained by Daniel Dalthorp. Last updated 2 years ago.
3.8 match 7 stars 7.81 score 55 scripts 2 dependents
fvafrcu
fakemake:Mock the Unix Make Utility
Use R as a minimal build system. This might come in handy if you are developing R packages and can not use a proper build system. Stay away if you can (use a proper build system).
Maintained by Andreas Dominik Cullmann. Last updated 2 years ago.
6.9 match 4.22 score 11 scripts 1 dependents
rnabioco
ggtrace:Trace and Highlight Groups of Data Points
Provides 'ggplot2' geoms that allow groups of data points to be outlined or highlighted for emphasis. This is particularly useful when working with dense datasets that are prone to overplotting.
Maintained by Ryan Sheridan. Last updated 1 years ago.
ggplot2ggplot2-geomvisualization
4.5 match 15 stars 6.06 score 38 scriptsdarwin-eu
DrugUtilisation:Summarise Patient-Level Drug Utilisation in Data Mapped to the OMOP Common Data Model
Summarise patient-level drug utilisation cohorts using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. New users and prevalent users cohorts can be generated and their characteristics, indication and drug use summarised.
Maintained by Martí Català. Last updated 2 months ago.
3.3 match 8.20 score 156 scripts 2 dependentsbioc
SingleR:Reference-Based Single-Cell RNA-Seq Annotation
Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.
Maintained by Aaron Lun. Last updated 1 months ago.
softwaresinglecellgeneexpressiontranscriptomicsclassificationclusteringannotationbioconductorsinglercpp
2.0 match 184 stars 12.83 score 2.1k scripts 2 dependents
insightsengineering
cards:Analysis Results Data
Construct CDISC (Clinical Data Interchange Standards Consortium) compliant Analysis Results Data objects. These objects are used and re-used to construct summary tables, visualizations, and written reports. The package also exports utilities for working with these objects and creating new Analysis Results Data objects.
Maintained by Daniel D. Sjoberg. Last updated 30 days ago.
2.3 match 40 stars 11.40 score 100 scripts 19 dependentsbioc
scuttle:Single-Cell RNA-Seq Analysis Utilities
Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.
Maintained by Aaron Lun. Last updated 5 months ago.
immunooncologysinglecellrnaseqqualitycontrolpreprocessingnormalizationtranscriptomicsgeneexpressionsequencingsoftwaredataimportopenblascpp
2.3 match 10.16 score 1.7k scripts 83 dependents
mvogel78
childsds:Data and Methods Around Reference Values in Pediatrics
Calculation of standard deviation scores and percentiles adduced from different standards (WHO, UK, Germany, Italy, China, etc). Also, references for laboratory values in children and adults are available, e.g., serum lipids, iron-related blood parameters, IGF, liver enzymes. See package documentation for full list.
Maintained by Mandy Vogel. Last updated 5 days ago.
6.5 match 3.49 score 51 scripts
nifu-no
saros.base:Base Tools for Semi-Automatic Reporting of Ordinary Surveys
Scaffold an entire web-based report using template chunks, based on a small chapter overview and a dataset. Highly adaptable with prefixes, suffixes, translations, etc. Also contains tools for password-protecting, e.g. for each organization's report on a website. Developed for the common case of a survey across multiple organizations/sites where each organization wants to obtain results for their organization compared with everyone else. See 'saros' (<https://CRAN.R-project.org/package=saros>) for tools used for authors in the drafted reports.
Maintained by Stephan Daus. Last updated 2 months ago.
3.6 match 1 stars 5.98 score 7 scriptsbioc
ReportingTools:Tools for making reports in various formats
The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. For more examples, please visit our site: http:// research-pub.gene.com/ReportingTools.
Maintained by Jason A. Hackney. Last updated 5 months ago.
immunooncologysoftwarevisualizationmicroarrayrnaseqgodatarepresentationgenesetenrichment
3.4 match 6.23 score 93 scripts 1 dependents
jprybylski
xpose.xtras:Extra Functionality for the 'xpose' Package
Adding some at-present missing functionality, or functions unlikely to be added to the base 'xpose' package. This includes some diagnostic plots that have been missing in translation from 'xpose4', but also some useful features that truly extend the capabilities of what can be done with 'xpose'. These extensions include the concept of a set of 'xpose' objects, and diagnostics for likelihood-based models.
Maintained by John Prybylski. Last updated 4 months ago.
3.4 match 6.01 score 5 scripts
nflverse
nflreadr:Download 'nflverse' Data
A minimal package for downloading data from 'GitHub' repositories of the 'nflverse' project.
Maintained by Tan Ho. Last updated 4 months ago.
nflnflfastrnflversesports-data
1.6 match 67 stars 12.29 score 476 scripts 10 dependentsbioc
BASiCS:Bayesian Analysis of Single-Cell Sequencing data
Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori, e.g. experimental conditions or cell types). BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells. Unlike traditional differential expression tools, BASiCS quantifies changes in expression that lie beyond comparisons of means, also allowing the study of changes in cell-to-cell heterogeneity. The latter can be quantified via a biological over-dispersion parameter that measures the excess of variability that is observed with respect to Poisson sampling noise, after normalisation and technical noise removal. Due to the strong mean/over-dispersion confounding that is typically observed for scRNA-seq datasets, BASiCS also tests for changes in residual over-dispersion, defined by residual values with respect to a global mean/over-dispersion trend.
Maintained by Catalina Vallejos. Last updated 5 months ago.
immunooncologynormalizationsequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecelldifferentialexpressionbayesiancellbiologybioconductor-packagegene-expressionrcpprcpparmadilloscrna-seqsingle-cellopenblascppopenmp
1.9 match 83 stars 10.14 score 368 scripts 1 dependents
johncoene
packer:An Opinionated Framework for Using 'JavaScript'
Enforces good practice and provides convenience functions to make work with 'JavaScript' not just easier but also scalable. It is a robust wrapper to 'NPM', 'yarn', and 'webpack' that enables to compartmentalize 'JavaScript' code, leverage 'NPM' and 'yarn' packages, include 'TypeScript', 'React', or 'Vue' in web applications, and much more.
Maintained by John Coene. Last updated 8 months ago.
3.0 match 148 stars 6.25 score 1 scripts 2 dependents
ketchbrookanalytics
migrate:Create Credit State Migration (Transition) Matrices
Tools to help convert credit risk data at two timepoints into traditional credit state migration (aka, "transition") matrices. At a higher level, 'migrate' is intended to help an analyst understand how risk moved in their credit portfolio over a time interval. References to this methodology include: 1. Schuermann, T. (2008) <doi:10.1002/9780470061596.risk0409>. 2. Perederiy, V. (2017) <doi:10.48550/arXiv.1708.00062>.
Maintained by Michael Thomas. Last updated 9 months ago.
credit-riskfinancerisk-management
3.1 match 6 stars 5.89 score 13 scripts
rte-antares-rpackage
antaresEditObject:Edit an 'Antares' Simulation
Edit an 'Antares' simulation before running it : create new areas, links, thermal clusters or binding constraints or edit existing ones. Update 'Antares' general & optimization settings. 'Antares' is an open source power system generator, more information available here : <https://antares-simulator.org/>.
Maintained by Tatiana Vargas. Last updated 1 months ago.
antares-simulationclusterenergymonte-carlo-simulationrte
2.0 match 8 stars 8.66 score 101 scripts
kapelner
PTE:Personalized Treatment Evaluator
We provide inference for personalized medicine models. Namely, we answer the questions: (1) how much better does a purported personalized recommendation engine for treatments do over a business-as-usual approach and (2) is that difference statistically significant?
Maintained by Adam Kapelner. Last updated 6 years ago.
7.2 match 2.37 score 26 scripts
ambiorix-web
ambiorix:Web Framework Inspired by 'Express.js'
A web framework inspired by 'express.js' to build any web service from multi-page websites to 'RESTful' application programming interfaces.
Maintained by John Coene. Last updated 16 days ago.
2.3 match 212 stars 7.28 score 8 dependents
dslc-io
tidytuesdayR:Access the Weekly 'TidyTuesday' Project Dataset
'TidyTuesday' is a project by the 'Data Science Learning Community' in which they post a weekly dataset in a public data repository (<https://github.com/rfordatascience/tidytuesday>) for people to analyze and visualize. This package provides the tools to easily download this data and the description of the source.
Maintained by Jon Harmon. Last updated 6 days ago.
1.6 match 77 stars 10.13 score 3.0k scriptsdarwin-eu
visOmopResults:Graphs and Tables for OMOP Results
Provides methods to transform omop_result objects into formatted tables and figures, facilitating the visualisation of study results working with the Observational Medical Outcomes Partnership (OMOP) Common Data Model.
Maintained by Núria Mercadé-Besora. Last updated 11 days ago.
1.8 match 7.89 score 53 scripts 3 dependents
vp-biostat
comorbidPGS:Assessing Predisposition Between Phenotypes using Polygenic Scores
Using polygenic scores (PGS, or PRS/GRS for binary outcomes), this package allows to investigate shared predisposition between different conditions, and do fast association analysis, export plots and views of the PGS distribution using 'ggplot2' object.
Maintained by Vincent Pascat. Last updated 3 months ago.
3.8 match 3 stars 3.78 score 3 scriptsdarwin-eu
CohortCharacteristics:Summarise and Visualise Characteristics of Patients in the OMOP CDM
Summarise and visualise the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model (CDM).
Maintained by Marti Catala. Last updated 4 months ago.
1.8 match 1 stars 8.03 score 111 scripts 1 dependents
richelbilderbeek
pureseqtmr:Predict Transmembrane Protein Topology
Proteins reside in either the cell plasma or in the cell membrane. A membrane protein goes through the membrane at least once. Given the amino acid sequence of a membrane protein, the tool 'PureseqTM' (<https://github.com/PureseqTM/pureseqTM_package>, as described in "Efficient And Accurate Prediction Of Transmembrane Topology From Amino acid sequence only.", Wang, Qing, et al (2019), <doi:10.1101/627307>), can predict the topology of a membrane protein. This package allows one to use 'PureseqTM' from R.
Maintained by Richèl J.C. Bilderbeek. Last updated 2 years ago.
3.5 match 1 stars 3.90 score 16 scriptsohdsi
PhenotypeR:Assess Study Cohorts Using a Common Data Model
Phenotype study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model. Diagnostics are run at the database, code list, cohort, and population level to assess whether study cohorts are ready for research.
Maintained by Edward Burn. Last updated 14 hours ago.
1.8 match 3 stars 7.76 score 57 scriptsohdsi
CohortSymmetry:Sequence Symmetry Analysis Using the Observational Medical Outcomes Partnership Common Data Model
Calculating crude sequence ratio, adjusted sequence ratio and confidence intervals using data mapped to the Observational Medical Outcomes Partnership Common Data Model.
Maintained by Xihang Chen. Last updated 7 days ago.
1.8 match 1 stars 7.52 score 73 scripts
cran
ubair:Effects of External Conditions on Air Quality
Analyzes the impact of external conditions on air quality using counterfactual approaches, featuring methods for data preparation, modeling, and visualization.
Maintained by Imke Voss. Last updated 2 months ago.
4.0 match 3.18 score
dcousin3
superb:Summary Plots with Adjusted Error Bars
Computes standard error and confidence interval of various descriptive statistics under various designs and sampling schemes. The main function, superb(), return a plot. It can also be used to obtain a dataframe with the statistics and their precision intervals so that other plotting environments (e.g., Excel) can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109> or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005) <doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012) <doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>, Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding <doi:10.20982/tqmp.15.1.p001> for specific references.
Maintained by Denis Cousineau. Last updated 2 months ago.
error-barsplottingstatisticssummary-plotssummary-statisticsvisualization
1.3 match 19 stars 9.53 score 155 scripts 2 dependentsdarwin-eu
DrugExposureDiagnostics:Diagnostics for OMOP Common Data Model Drug Records
Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Maintained by Ger Inberg. Last updated 18 days ago.
1.8 match 4 stars 7.11 score 41 scripts
canmod
iidda:Processing Infectious Disease Datasets in IIDDA.
Part of an open toolchain for processing infectious disease datasets available through the IIDDA data repository.
Maintained by Steve Walker. Last updated 4 months ago.
2.0 match 6.02 score 133 scripts 3 dependents
hermitz9
FusionLearn:Fusion Learning
The fusion learning method uses a model selection algorithm to learn from multiple data sets across different experimental platforms through group penalization. The responses of interest may include a mix of discrete and continuous variables. The responses may share the same set of predictors, however, the models and parameters differ across different platforms. Integrating information from different data sets can enhance the power of model selection. Package is based on Xin Gao, Raymond J. Carroll (2017) <arXiv:1610.00667v1>.
Maintained by Yuan Zhong. Last updated 3 years ago.
6.0 match 2.00 score 6 scriptsrstudio
plumbertableau:Turn 'Plumber' APIs into 'Tableau' Extensions
Build 'Plumber' APIs that can be used in 'Tableau' workbooks. Annotations in R comments allow APIs to conform to the 'Tableau Analytics Extension' specification, so that R code can be used to power 'Tableau' workbooks.
Maintained by James Blair. Last updated 1 years ago.
1.7 match 30 stars 6.74 score 23 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 14 days ago.
systemsbiologysinglecelltranscriptomicsnetwork
1.8 match 5 stars 6.20 score 5 scriptsfvafrcu
fritools:Utilities for the Forest Research Institute of the State Baden-Wuerttemberg
Miscellaneous utilities, tools and helper functions for finding and searching files on disk, searching for and removing R objects from the workspace. Does not import or depend on any third party package, but on core R only (i.e. it may depend on packages with priority 'base').
Maintained by Andreas Dominik Cullmann. Last updated 1 months ago.
1.9 match 5.82 score 4 scripts 6 dependentscran
sleev:Semiparametric Likelihood Estimation with Errors in Variables
Efficient regression analysis under general two-phase sampling, where Phase I includes error-prone data and Phase II contains validated data on a subset.
Maintained by Ran Tao. Last updated 4 months ago.
4.0 match 2.70 scorebioc
QTLExperiment:S4 classes for QTL summary statistics and metadata
QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It is based on the 'SummarizedExperiment' class and contains functions for creating, merging, and subsetting objects. 'QTLExperiment' also stores experiment metadata and has checks in place to ensure that transformations apply correctly.
Maintained by Amelia Dunstone. Last updated 12 days ago.
functionalgenomicsdataimportdatarepresentationinfrastructuresequencingsnpsoftware
1.9 match 2 stars 5.32 score 14 scripts 1 dependents
kevinstadler
cultevo:Tools, Measures and Statistical Tests for Cultural Evolution
Provides tools and statistics useful for analysing data from artificial language experiments. It implements the information-theoretic measure of the compositionality of signalling systems due to Spike (2016) <http://hdl.handle.net/1842/25930>, the Mantel test for distance matrix correlation (after Dietz 1983) <doi:10.1093/sysbio/32.1.21>), functions for computing string and meaning distance matrices as well as an implementation of the Page test for monotonicity of ranks (Page 1963) <doi:10.1080/01621459.1963.10500843> with exact p-values up to k = 22.
Maintained by Kevin Stadler. Last updated 1 years ago.
1.3 match 8 stars 6.50 score 131 scripts 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 12 months ago.
3.6 match 2.28 score 38 scriptsbioc
benchdamic:Benchmark of differential abundance methods on microbiome data
Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method's distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.
Maintained by Matteo Calgaro. Last updated 4 months ago.
metagenomicsmicrobiomedifferentialexpressionmultiplecomparisonnormalizationpreprocessingsoftwarebenchmarkdifferential-abundance-methods
1.3 match 8 stars 5.78 score 8 scriptsbioc
cydar:Using Mass Cytometry for Differential Abundance Analyses
Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.
Maintained by Aaron Lun. Last updated 5 months ago.
immunooncologyflowcytometrymultiplecomparisonproteomicssinglecellcpp
1.3 match 5.64 score 48 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 2 months ago.
1.8 match 4 stars 4.00 score 1 scriptscran
CohortSurvival:Estimate Survival from Common Data Model Cohorts
Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
Maintained by Kim López-Güell. Last updated 12 days ago.
1.7 match 4.08 scorecran
ambiorix:Web Framework Inspired by 'Express.js'
A web framework inspired by 'express.js' to build any web service from multi-page websites to 'RESTful' application programming interfaces.
Maintained by John Coene. Last updated 16 days ago.
2.3 match 3.08 score 8 dependents
jonthegeek
mockplumber:Mock servers from 'API' documentation
Create a 'plumber' file from an 'OpenAPI' document defining an 'API'. The 'plumber' file will have all the information to generate a mock server for that 'API'.
Maintained by Jon Harmon. Last updated 2 years ago.
3.7 match 1 stars 1.70 scorehermitz9
HMTL:Heterogeneous Multi-Task Feature Learning
The heterogeneous multi-task feature learning is a data integration method to conduct joint feature selection across multiple related data sets with different distributions. The algorithm can combine different types of learning tasks, including linear regression, Huber regression, adaptive Huber, and logistic regression. The modified version of Bayesian Information Criterion (BIC) is produced to measure the model performance. Package is based on Yuan Zhong, Wei Xu, and Xin Gao (2022) <https://www.fields.utoronto.ca/talk-media/1/53/65/slides.pdf>.
Maintained by Yuan Zhong. Last updated 2 years ago.
6.0 match 1.00 score
gcicc
figuRes2:Support for a Variety of Figure Production Tasks
We view a figure as a collection of graphs/tables assembled on a page and optionally annotated with metadata (titles, headers and footers). Functions and supporting documentation are offered to streamline a variety of figure production task.
Maintained by Greg Cicconetti. Last updated 3 years ago.
1.2 match 3 stars 4.78 score
vavrycuk-zz
PoDBAY:Vaccine Efficacy Estimation Package
Set of functions that implement the PoDBAY method, described in the publication 'A method to estimate probability of disease and vaccine efficacy from clinical trial immunogenicity data' by Julie Dudasova, Regina Laube, Chandni Valiathan, Matthew C. Wiener, Ferdous Gheyas, Pavel Fiser, Justina Ivanauskaite, Frank Liu and Jeffrey R. Sachs (NPJ Vaccines, 2021), <doi:10.1038/s41541-021-00377-6>.
Maintained by Julie Dudasova (MSD). Last updated 4 years ago.
1.5 match 3.30 score 10 scriptsmerck
metalite:ADaM Metadata Structure
A metadata structure for clinical data analysis and reporting based on Analysis Data Model (ADaM) datasets. The package simplifies clinical analysis and reporting tool development by defining standardized inputs, outputs, and workflow. The package can be used to create analysis and reporting planning grid, mock table, and validated analysis and reporting results based on consistent inputs.
Maintained by Yujie Zhao. Last updated 7 months ago.
0.5 match 15 stars 8.89 score 57 scripts 5 dependents
aalfons
r2spss:Format R Output to Look Like SPSS
Create plots and LaTeX tables that look like SPSS output for use in teaching materials. Rather than copying-and-pasting SPSS output into documents, R code that mocks up SPSS output can be integrated directly into dynamic LaTeX documents with tools such as knitr. Functionality includes statistical techniques that are typically covered in introductory statistics classes: descriptive statistics, common hypothesis tests, ANOVA, and linear regression, as well as box plots, histograms, scatter plots, and line plots (including profile plots).
Maintained by Andreas Alfons. Last updated 3 years ago.
0.5 match 3 stars 4.18 score 1 scripts
jayqi
spongebob:SpongeBob-Case Converter : spOngEboB-CASe CoNVertER
Convert text (and text in R objects) to Mocking SpongeBob case <https://knowyourmeme.com/memes/mocking-spongebob> and show them off in fun ways. CoNVErT TexT (AnD TeXt In r ObJeCtS) To MOCkINg SpoNgebOb CAsE <https://knowyourmeme.com/memes/mocking-spongebob> aND shOw tHem OFf IN Fun WayS.
Maintained by Jay Qi. Last updated 6 years ago.
1.0 match 1 stars 1.70 score 6 scripts