R-universe search: needs:remotes

r-lib

devtools:Tools to Make Developing R Packages Easier

Collection of package development tools.

Maintained by Jennifer Bryan. Last updated 6 months ago.

package-creation

2.4k stars 19.55 score 51k scripts 150 dependents

trinker

pacman:Package Management Tool

Tools to more conveniently perform tasks associated with add-on packages. pacman conveniently wraps library and package related functions and names them in an intuitive and consistent fashion. It seeks to combine functionality from lower level functions which can speed up workflow.

Maintained by Tyler Rinker. Last updated 5 years ago.

github package-management packages

314 stars 14.25 score 14k scripts 10 dependents

covid19datahub

COVID19:COVID-19 Data Hub

Unified datasets for a better understanding of COVID-19.

Maintained by Emanuele Guidotti. Last updated 1 months ago.

2019-ncov coronavirus covid-19 covid-data covid19-data

252 stars 11.08 score 265 scripts

ropensci

goodpractice:Advice on R Package Building

Give advice about good practices when building R packages. Advice includes functions and syntax to avoid, package structure, code complexity, code formatting, etc.

Maintained by Mark Padgham. Last updated 4 months ago.

467 stars 10.32 score 79 scripts 2 dependents

opencpu

opencpu:Producing and Reproducing Results

A system for embedded scientific computing and reproducible research with R. The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange with R. This provides a reliable and scalable foundation for statistical services or building R web applications. The OpenCPU server runs either as a single-user development server within the interactive R session, or as a multi-user Linux stack based on Apache2. The entire system is fully open source and permissively licensed. The OpenCPU website has detailed documentation and example apps.

Maintained by Jeroen Ooms. Last updated 6 months ago.

733 stars 10.17 score 168 scripts 2 dependents

lmullen

gender:Predict Gender from Names Using Historical Data

Infers state-recorded gender categories from first names and dates of birth using historical datasets. By using these datasets instead of lists of male and female names, this package is able to more accurately infer the gender of a name, and it is able to report the probability that a name was male or female. GUIDELINES: This method must be used cautiously and responsibly. Please be sure to see the guidelines and warnings about usage in the 'README' or the package documentation. See Blevins and Mullen (2015) <http://www.digitalhumanities.org/dhq/vol/9/3/000223/000223.html>.

Maintained by Lincoln Mullen. Last updated 3 years ago.

189 stars 9.80 score 265 scripts 7 dependents

trinker

qdap:Bridging the Gap Between Qualitative Data and Quantitative Analysis

Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R packages that undertake higher level analysis and visualization of text. This affords the user a more efficient and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other areas of Text Mining/ Natural Language Processing.

Maintained by Tyler Rinker. Last updated 5 years ago.

qdap quantitative-discourse-analysis text-analysis text-mining text-plotting openjdk

176 stars 9.61 score 1.3k scripts 3 dependents

thinkr-open

fusen:Build a Package from Rmarkdown Files

Use Rmarkdown First method to build your package. Start your package with documentation, functions, examples and tests in the same unique file. Everything can be set from the Rmarkdown template file provided in your project, then inflated as a package. Inflating the template copies the relevant chunks and sections in the appropriate files required for package development.

Maintained by Vincent Guyader. Last updated 2 months ago.

hacktoberfest rmd-first

163 stars 9.45 score 35 scripts

briencj

asremlPlus:Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences

Assists in automating the selection of terms to include in mixed models when 'asreml' is used to fit the models. Procedures are available for choosing models that conform to the hierarchy or marginality principle, for fitting and choosing between two-dimensional spatial models using correlation, natural cubic smoothing spline and P-spline models. A history of the fitting of a sequence of models is kept in a data frame. Also used to compute functions and contrasts of, to investigate differences between and to plot predictions obtained using any model fitting function. The content falls into the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model selection and description functions, (iv) Model diagnostics and simulation functions, (v) Prediction production and presentation functions, (vi) Response transformation functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions (for further details see 'asremlPlus-package' in help). The 'asreml' package provides a computationally efficient algorithm for fitting a wide range of linear mixed models using Residual Maximum Likelihood. It is a commercial package and a license for it can be purchased from 'VSNi' <https://vsni.co.uk/> as 'asreml-R', who will supply a zip file for local installation/updating (see <https://asreml.kb.vsni.co.uk/>). It is not needed for functions that are methods for 'alldiffs' and 'data.frame' objects. The package 'asremPlus' can also be installed from <http://chris.brien.name/rpackages/>.

Maintained by Chris Brien. Last updated 1 months ago.

asreml mixed-models

19 stars 9.37 score 200 scripts

r-spatial

link2GI:Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools

Functions and tools for using open GIS and remote sensing command-line interfaces in a reproducible environment.

Maintained by Chris Reudenbach. Last updated 4 months ago.

26 stars 8.99 score 78 scripts 1 dependents

pharmar

riskmetric:Risk Metrics to Evaluating R Packages

Facilities for assessing R packages against a number of metrics to help quantify their robustness.

Maintained by Eli Miller. Last updated 7 days ago.

166 stars 8.98 score 43 scripts

ajrgodfrey

BrailleR:Improved Access for Blind Users

Blind users do not have access to the graphical output from R without printing the content of graphics windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R. This includes the text descriptions of graphs, convenience functions to replace the functionality offered in many GUI front ends, and experimental functionality for optimising graphical content to prepare it for embossing as tactile images.

Maintained by A. Jonathan R. Godfrey. Last updated 12 months ago.

123 stars 8.90 score 143 scripts

ropensci

codemetar:Generate 'CodeMeta' Metadata for R Packages

The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.

Maintained by Carl Boettiger. Last updated 2 months ago.

metadata codemeta ropensci citation credit linked-data json-ld peer-reviewed

68 stars 8.90 score 34 scripts 6 dependents

pik-piam

remind2:The REMIND R package (2nd generation)

Contains the REMIND-specific routines for data and model output manipulation.

Maintained by Renato Rodrigues. Last updated 3 days ago.

8.87 score 161 scripts 5 dependents

cynkra

fledge:Smoother Change Tracking and Versioning for R Packages

Streamlines the process of updating changelogs (NEWS.md) and versioning R packages developed in git repositories.

Maintained by Kirill Müller. Last updated 3 months ago.

changelog git package-creation

188 stars 8.73 score 10 scripts

ramikrispin

coronavirus:The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset

Provides a daily summary of the Coronavirus (COVID-19) cases by state/province. Data source: Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus <https://systems.jhu.edu/research/public-health/ncov/>.

Maintained by Rami Krispin. Last updated 2 years ago.

covid-19 covid19 covid19-data dataset

499 stars 8.25 score 716 scripts

rcannood

SCORPIUS:Inferring Developmental Chronologies from Single-Cell RNA Sequencing Data

An accurate and easy tool for performing linear trajectory inference on single cells using single-cell RNA sequencing data. In addition, 'SCORPIUS' provides functions for discovering the most important genes with respect to the reconstructed trajectory, as well as nice visualisation tools. Cannoodt et al. (2016) <doi:10.1101/079509>.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

59 stars 8.17 score 126 scripts

tychobra

polished:Authentication and Hosting for 'shiny' Apps

Authentication, user administration, hosting, and additional infrastructure for 'shiny' apps. See <https://polished.tech> for additional documentation and examples.

Maintained by Andy Merlino. Last updated 11 days ago.

233 stars 8.09 score 75 scripts

pakillo

grateful:Facilitate Citation of R Packages

Facilitates the citation of R packages used in analysis projects. Scans project for packages used, gets their citations, and produces a document with citations in the preferred bibliography format, ready to be pasted into reports or manuscripts. Alternatively, 'grateful' can be used directly within an 'R Markdown' or 'Quarto' document.

Maintained by Francisco Rodriguez-Sanchez. Last updated 17 days ago.

citation-generator software-citation

229 stars 8.04 score 269 scripts

mazamascience

MazamaSpatialUtils:Spatial Data Download and Utility Functions

A suite of conversion functions to create internally standardized spatial polygons data frames. Utility functions use these data sets to return values such as country, state, time zone, watershed, etc. associated with a set of longitude/latitude pairs. (They also make cool maps.)

Maintained by Jonathan Callahan. Last updated 5 months ago.

5 stars 8.01 score 282 scripts 2 dependents

matloff

dsld:Data Science Looks at Discrimination

Statistical and graphical tools for detecting and measuring discrimination and bias, be it racial, gender, age or other. Detection and remediation of bias in machine learning algorithms. 'Python' interfaces available.

Maintained by Norm Matloff. Last updated 2 months ago.

12 stars 7.81 score 35 scripts

mazamascience

MazamaCoreUtils:Utility Functions for Production R Code

A suite of utility functions providing functionality commonly needed for production level projects such as logging, error handling, cache management and date-time parsing. Functions for date-time parsing and formatting require that time zones be specified explicitly, avoiding a common source of error when working with environmental time series.

Maintained by Jonathan Callahan. Last updated 4 months ago.

4 stars 7.76 score 119 scripts 5 dependents

daattali

addinslist:Discover and Install Useful RStudio Addins

Browse through a continuously updated list of existing RStudio addins and install/uninstall their corresponding packages.

Maintained by Dean Attali. Last updated 8 months ago.

850 stars 7.73 score 18 scripts

bioc

phantasus:Visual and interactive gene expression analysis

Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

Maintained by Alexey Sergushichev. Last updated 5 months ago.

geneexpression gui visualization datarepresentation transcriptomics rnaseq microarray normalization clustering differentialexpression principalcomponent immunooncology

43 stars 7.68 score 15 scripts

desiquintans

librarian:Install, Update, Load Packages from CRAN, 'GitHub', and 'Bioconductor' in One Step

Automatically install, update, and load 'CRAN', 'GitHub', and 'Bioconductor' packages in a single function call. By accepting bare unquoted names for packages, it's easy to add or remove packages from the list.

Maintained by Desi Quintans. Last updated 3 months ago.

53 stars 7.64 score 410 scripts 1 dependents

ropensci

tic:Tasks Integrating Continuously: CI-Agnostic Workflow Definitions

Provides a way to describe common build and deployment workflows for R-based projects: packages, websites (e.g. blogdown, pkgdown), or data processing (e.g. research compendia). The recipe is described independent of the continuous integration tool used for processing the workflow (e.g. 'GitHub Actions' or 'Circle CI'). This package has been peer-reviewed by rOpenSci (v0.3.0.9004).

Maintained by Eli Miller. Last updated 2 months ago.

appveyor continuous-integration deployment githubactions travis-ci

155 stars 7.57 score 16 scripts

dynverse

dyngen:A Multi-Modal Simulator for Spearheading Single-Cell Omics Analyses

A novel, multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. 'dyngen' is more flexible than current single-cell simulation engines. It allows better method development and benchmarking, thereby stimulating development and testing of novel computational methods. Cannoodt et al. (2021) <doi:10.1038/s41467-021-24152-2>.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

benchmarking single-cell single-cell-analysis single-cell-omics

74 stars 7.53 score 57 scripts

dynverse

dynwrap:Representing and Inferring Single-Cell Trajectories

Provides functionality to infer trajectories from single-cell data, represent them into a common format, and adapt them. Other biological information can also be added, such as cellular grouping, RNA velocity and annotation. Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

trajectory-inference

16 stars 7.48 score 159 scripts 1 dependents

bioc

cogena:co-expressed gene-set enrichment analysis

cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.

Maintained by Zhilong Jia. Last updated 5 months ago.

clustering genesetenrichment geneexpression visualization pathways kegg go microarray sequencing systemsbiology datarepresentation dataimport bioconductor bioinformatics

12 stars 7.36 score 32 scripts

hoxo-m

githubinstall:A Helpful Way to Install R Packages Hosted on GitHub

Provides an helpful way to install packages hosted on GitHub.

Maintained by Koji Makiyama. Last updated 7 years ago.

r-language

49 stars 7.29 score 177 scripts

inbo

checklist:A Thorough and Strict Set of Checks for R Packages and Source Code

An opinionated set of rules for R packages and R source code projects.

Maintained by Thierry Onkelinx. Last updated 1 months ago.

checklist continuous-integration continuous-testing quality-assurance

19 stars 7.24 score 21 scripts 2 dependents

pik-piam

lucode2:Code Manipulation and Analysis Tools

A collection of tools which allow to manipulate and analyze code.

Maintained by Jan Philipp Dietrich. Last updated 10 days ago.

7.22 score 364 scripts 8 dependents

ropensci

pkgcheck:rOpenSci Package Checks

Check whether a package is ready for submission to rOpenSci's peer review system.

Maintained by Mark Padgham. Last updated 20 days ago.

compliance-automation software-analysis software-checking

19 stars 7.13 score 29 scripts 1 dependents

r-lib

roxygen2md:'Roxygen' to 'Markdown'

Converts elements of 'roxygen' documentation to 'markdown'.

Maintained by Kirill Müller. Last updated 4 months ago.

documentation markdown

68 stars 7.00 score 11 scripts 2 dependents

thinkr-open

thinkr:Tools for Cleaning Up Messy Files

Some tools for cleaning up messy 'Excel' files to be suitable for R. People who have been working with 'Excel' for years built more or less complicated sheets with names, characters, formats that are not homogeneous. To be able to use them in R nowadays, we built a set of functions that will avoid the majority of importation problems and keep all the data at best.

Maintained by Vincent Guyader. Last updated 3 years ago.

hacktoberfest thinkr-not-maintained

29 stars 6.96 score 45 scripts

dynverse

dynutils:Common Functionality for the 'dynverse' Packages

Provides common functionality for the 'dynverse' packages. 'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods. For more information, check out <https://dynverse.org>.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

cpp

3 stars 6.89 score 109 scripts 8 dependents

cargomoose

ggraptR:Allows Interactive Visualization of Data Through a Web Browser GUI

Intended for both technical and non-technical users to create interactive data visualizations through a web browser GUI without writing any code.

Maintained by Eugene Dubossarsky. Last updated 5 years ago.

76 stars 6.88 score 66 scripts

pik-piam

edgeTransport:Prepare EDGE Transport Data for the REMIND model

EDGE-T is a fork of the GCAM transport module https://jgcri.github.io/gcam-doc/energy.html#transportation with a high level of detail in its representation of technological and modal options. It is a partial equilibrium model with a nested multinomial logit structure and relies on the modified logit formulation. Most of the sources are not publicly available. PIK-internal users can find the sources in the distributed file system in the folder `/p/projects/rd3mod/inputdata/sources/EDGE-Transport-Standalone`.

Maintained by Johanna Hoppe. Last updated 2 days ago.

5 stars 6.84 score 16 scripts 2 dependents

kozodoi

fairness:Algorithmic Fairness Metrics

Offers calculation, visualization and comparison of algorithmic fairness metrics. Fair machine learning is an emerging topic with the overarching aim to critically assess whether ML algorithms reinforce existing social biases. Unfair algorithms can propagate such biases and produce predictions with a disparate impact on various sensitive groups of individuals (defined by sex, gender, ethnicity, religion, income, socioeconomic status, physical or mental disabilities). Fair algorithms possess the underlying foundation that these groups should be treated similarly or have similar prediction outcomes. The fairness R package offers the calculation and comparisons of commonly and less commonly used fairness metrics in population subgroups. These methods are described by Calders and Verwer (2010) <doi:10.1007/s10618-010-0190-x>, Chouldechova (2017) <doi:10.1089/big.2016.0047>, Feldman et al. (2015) <doi:10.1145/2783258.2783311> , Friedler et al. (2018) <doi:10.1145/3287560.3287589> and Zafar et al. (2017) <doi:10.1145/3038912.3052660>. The package also offers convenient visualizations to help understand fairness metrics.

Maintained by Nikita Kozodoi. Last updated 2 years ago.

algorithmic-discrimination algorithmic-fairness discrimination disparate-impact fairness fairness-ai fairness-ml machine-learning

32 stars 6.82 score 69 scripts 1 dependents

rcannood

GillespieSSA2:Gillespie's Stochastic Simulation Algorithm for Impatient People

A fast, scalable, and versatile framework for simulating large systems with Gillespie's Stochastic Simulation Algorithm ('SSA'). This package is the spiritual successor to the 'GillespieSSA' package originally written by Mario Pineda-Krch. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended. Cannoodt and Saelens et al. (2021) <doi:10.1038/s41467-021-24152-2>.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

cpp

8 stars 6.79 score 51 scripts 1 dependents

merck

pkglite:Compact Package Representations

A tool, grammar, and standard to represent and exchange R package source code as text files. Converts one or more source packages to a text file and restores the package structures from the file.

Maintained by Nan Xiao. Last updated 5 months ago.

clinical-trials ectd packaging-tool pharmaverse

29 stars 6.75 score 12 scripts

thinkr-open

checkhelper:Deal with Check Outputs

Deal with packages 'check' outputs and reduce the risk of rejection by 'CRAN' by following policies.

Maintained by Sebastien Rochette. Last updated 1 years ago.

34 stars 6.74 score 18 scripts

frbcesab

rcompendium:Create a Package or Research Compendium Structure

Makes easier the creation of R package or research compendium (i.e. a predefined files/folders structure) so that users can focus on the code/analysis instead of wasting time organizing files. A full ready-to-work structure is set up with some additional features: version control, remote repository creation, CI/CD configuration (check package integrity under several OS, test code with 'testthat', and build and deploy website using 'pkgdown'). This package heavily relies on the R packages 'devtools' and 'usethis' and follows recommendations made by Wickham H. (2015) <ISBN:9781491910597> and Marwick B. et al. (2018) <doi:10.7287/peerj.preprints.3192v2>.

Maintained by Nicolas Casajus. Last updated 2 months ago.

reproducible-research research-compendium

40 stars 6.72 score 22 scripts

correlaid

newsanchor:Client for the News API

Interface to gather news from the 'News API', based on a multilevel query <https://newsapi.org/>. A personal API key is required.

Maintained by Yannik Buhl. Last updated 5 years ago.

36 stars 6.70 score 40 scripts

mazamascience

AirMonitor:Air Quality Data Analysis

Utilities for working with hourly air quality monitoring data with a focus on small particulates (PM2.5). A compact data model is structured as a list with two dataframes. A 'meta' dataframe contains spatial and measuring device metadata associated with deployments at known locations. A 'data' dataframe contains a 'datetime' column followed by columns of measurements associated with each "device-deployment". Algorithms to calculate NowCast and the associated Air Quality Index (AQI) are defined at the US Environmental Projection Agency AirNow program: <https://document.airnow.gov/technical-assistance-document-for-the-reporting-of-daily-air-quailty.pdf>.

Maintained by Jonathan Callahan. Last updated 6 months ago.

7 stars 6.57 score 178 scripts

jakesherman

easypackages:Easy Loading and Installing of Packages

Easily load and install multiple packages from different sources, including CRAN and GitHub. The libraries function allows you to load or attach multiple packages in the same function call. The packages function will load one or more packages, and install any packages that are not installed on your system (after prompting you). Also included is a from_import function that allows you to import specific functions from a package into the global environment.

Maintained by Jake Sherman. Last updated 7 years ago.

packages

11 stars 6.52 score 490 scripts

gisma

uavRmp:UAV Mission Planner

The Unmanned Aerial Vehicle Mission Planner provides an easy to use work flow for planning autonomous obstacle avoiding surveys of ready to fly unmanned aerial vehicles to retrieve aerial or spot related data. It creates either intermediate flight control files for the DJI-Litchi supported series or ready to upload control files for the pixhawk-based flight controller as used in the 3DR-Solo or Yuneec series. Additionally it contains some useful tools for digitizing and data manipulation.

Maintained by Chris Reudenbach. Last updated 10 months ago.

cultural-heritage dji drone flight-planning forest-mapping litchi low-budget-uav mission-planning photogrammetry pixhawk pixhawk-controller qgroundcontrol2litchi solo survey terrain-following terrain-mapping uavs yuneec

25 stars 6.48 score 6 scripts

atomashevic

transforEmotion:Sentiment Analysis for Text, Image and Video using Transformer Models

Implements sentiment analysis using huggingface <https://huggingface.co> transformer zero-shot classification model pipelines for text and image data. The default text pipeline is Cross-Encoder's DistilRoBERTa <https://huggingface.co/cross-encoder/nli-distilroberta-base> and default image/video pipeline is Open AI's CLIP <https://huggingface.co/openai/clip-vit-base-patch32>. All other zero-shot classification model pipelines can be implemented using their model name from <https://huggingface.co/models?pipeline_tag=zero-shot-classification>.

Maintained by Aleksandar Tomašević. Last updated 3 months ago.

26 stars 6.40 score 12 scripts

inbo

n2khab:Providing Preprocessed Reference Data for Flemish Natura 2000 Habitat Analyses

The n2khab package is an R package with preprocessing functions and standard reference data, useful for analyses regarding Flemish Natura 2000 habitats and regionally important biotopes (RIBs).

Maintained by Floris Vanderhaeghe. Last updated 3 months ago.

habitat natura2000 preprocessing-functions reproducibility

2 stars 6.32 score 139 scripts 1 dependents

gesistsa

rang:Reconstructing Reproducible R Computational Environments

Resolve the dependency graph of R packages at a specific time point based on the information from various 'R-hub' web services <https://blog.r-hub.io/>. The dependency graph can then be used to reconstruct the R computational environment with 'Rocker' <https://rocker-project.org>.

Maintained by Chung-hong Chan. Last updated 2 months ago.

reproducibility reproducible-research

80 stars 6.32 score 13 scripts

pik-piam

mrremind:MadRat REMIND Input Data Package

The mrremind packages contains data preprocessing for the REMIND model.

Maintained by Lavinia Baumstark. Last updated 3 days ago.

4 stars 6.25 score 15 scripts 1 dependents

iheid-library

iheiddown:For Writing Geneva Graduate Institute Documents

A set of tools for writing documents according to Geneva Graduate Institute conventions and regulations. The most common use is for writing and compiling theses or thesis chapters, as drafts or for examination with correct preamble formatting. However, the package also offers users to create HTML presentation slides with 'xaringan', complete problem sets, format posters, and, for course instructors, prepare a syllabus. The package includes additional functions for institutional color palettes, an institutional 'ggplot' theme, a function for counting manuscript words, and a bibliographical analysis toolkit.

Maintained by James Hollway. Last updated 2 years ago.

rmarkdown thesis university

11 stars 6.14 score 5 scripts

bioc

gDRstyle:A package with style requirements for the gDR suite

Package fills a helper package role for whole gDR suite. It helps to support good development practices by keeping style requirements and style tests for other packages. It also contains build helpers to make all package requirements met.

Maintained by Arkadiusz Gladki. Last updated 2 months ago.

software infrastructure

2 stars 6.10 score 2 scripts

ramikrispin

covid19italy:The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Italy Dataset

Provides a daily summary of the Coronavirus (COVID-19) cases in Italy by country, region and province level. Data source: Presidenza del Consiglio dei Ministri - Dipartimento della Protezione Civile <https://www.protezionecivile.it/>.

Maintained by Rami Krispin. Last updated 2 years ago.

47 stars 6.07 score 25 scripts

kforner

srcpkgs:R Source Packages Manager

Manage a collection/library of R source packages. Discover, document, load, test source packages. Enable to use those packages as if they were actually installed. Quickly reload only what is needed on source code change. Run tests and checks in parallel.

Maintained by Karl Forner. Last updated 10 months ago.

11 stars 6.04 score 6 scripts

bioc

INDEED:Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package

An R package for integrated differential expression and differential network analysis based on omic data for cancer biomarker discovery. Both correlation and partial correlation can be used to generate differential network to aid the traditional differential expression analysis to identify changes between biomolecules on both their expression and pairwise association levels. A detailed description of the methodology has been published in Methods journal (PMID: 27592383). An interactive visualization feature allows for the exploration and selection of candidate biomarkers.

Maintained by Ressom group. Last updated 5 months ago.

immunooncology software researchfield biologicalquestion statisticalmethod differentialexpression massspectrometry metabolomics

5 stars 6.02 score 10 scripts

ankane

jetpack:A Friendly Package Manager

Manage project dependencies from your DESCRIPTION file. Create a reproducible virtual environment with minimal additional files in your project. Provides tools to add, remove, and update dependencies as well as install existing dependencies with a single function.

Maintained by Andrew Kane. Last updated 13 days ago.

242 stars 5.96 score 19 scripts

bioc

PathoStat:PathoStat Statistical Microbiome Analysis Package

The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.

Maintained by Solaiappan Manimaran. Last updated 5 months ago.

microbiome metagenomics graphandnetwork microarray patternlogic principalcomponent sequencing software visualization rnaseq immunooncology

8 stars 5.90 score 8 scripts

gaborcsardi

cyclocomp:Cyclomatic Complexity of R Code

Cyclomatic complexity is a software metric (measurement), used to indicate the complexity of a program. It is a quantitative measure of the number of linearly independent paths through a program's source code. It was developed by Thomas J. McCabe, Sr. in 1976.

Maintained by Gabor Csardi. Last updated 2 years ago.

code-analysis complexity-measure

2 stars 5.88 score 22 scripts 5 dependents

jmzeng1314

AnnoProbe:annotate the gene symbols for probes in expression array

We curated 147 of expression array, from 3 species(human,mouse,rat), 3 companies(affymetrix,illumina,agilent), by aligning the fasta sequences of all probes of each platform to their corresponding reference genome, and then annotate them to genes.

Maintained by The package maintainer. Last updated 5 years ago.

105 stars 5.88 score 126 scripts

fdetsch

Orcs:Omnidirectional R Code Snippets

I tend to repeat the same code chunks over and over again. At first, this was fine for me and I paid little attention to such redundancies. A little later, when I got tired of manually replacing Linux filepaths with the referring Windows versions, and vice versa, I started to stuff some very frequently used work-steps into functions and, even later, into a proper R package. And that's what this package is - a hodgepodge of various R functions meant to simplify (my) everyday-life coding work without, at the same time, being devoted to a particular scope of application.

Maintained by Florian Detsch. Last updated 2 years ago.

cpp

5 stars 5.87 score 98 scripts

modeloriented

modelDown:Make Static HTML Website for Predictive Models

Website generator with HTML summaries for predictive models. This package uses 'DALEX' explainers to describe global model behavior. We can see how well models behave (tabs: Model Performance, Auditor), how much each variable contributes to predictions (tabs: Variable Response) and which variables are the most important for a given model (tabs: Variable Importance). We can also compare Concept Drift for pairs of models (tabs: Drifter). Additionally, data available on the website can be easily recreated in current R session. Work on this package was financially supported by the NCN Opus grant 2017/27/B/ST6/01307 at Warsaw University of Technology, Faculty of Mathematics and Information Science.

Maintained by Kamil Romaszko. Last updated 4 years ago.

121 stars 5.80 score 15 scripts

bioc

MetID:Network-based prioritization of putative metabolite IDs

This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by LC-MS.

Maintained by Zhenzhi Li. Last updated 5 months ago.

assaydomain biologicalquestion infrastructure researchfield statisticalmethod technology workflowstep network kegg

1 stars 5.74 score 110 scripts

tiago-simoes

EvoPhylo:Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

Performs automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses, following concepts introduced by Simões and Pierce (2021) <doi:10.1038/s41559-021-01532-x>.

Maintained by Tiago Simoes. Last updated 2 years ago.

4 stars 5.66 score 19 scripts

mazamascience

MazamaLocationUtils:Manage Spatial Metadata for Known Locations

Utility functions for discovering and managing metadata associated with spatially unique "known locations". Applications include all fields of environmental monitoring (e.g. air and water quality) where data are collected at stationary sites.

Maintained by Jonathan Callahan. Last updated 4 months ago.

5.64 score 108 scripts

cole-brokamp

automagic:Automagically Document and Install Packages Necessary to Run R Code

Parse R code in a given directory for R packages and attempt to install them from CRAN or GitHub. Optionally use a dependencies file for tighter control over which package versions to install.

Maintained by Cole Brokamp. Last updated 4 years ago.

57 stars 5.61 score 12 scripts 2 dependents

tomzylkin

penppml:Penalized Poisson Pseudo Maximum Likelihood Regression

A set of tools that enables efficient estimation of penalized Poisson Pseudo Maximum Likelihood regressions, using lasso or ridge penalties, for models that feature one or more sets of high-dimensional fixed effects. The methodology is based on Breinlich, Corradi, Rocha, Ruta, Santos Silva, and Zylkin (2021) <http://hdl.handle.net/10986/35451> and takes advantage of the method of alternating projections of Gaure (2013) <doi:10.1016/j.csda.2013.03.024> for dealing with HDFE, as well as the coordinate descent algorithm of Friedman, Hastie and Tibshirani (2010) <doi:10.18637/jss.v033.i01> for fitting lasso regressions. The package is also able to carry out cross-validation and to implement the plugin lasso of Belloni, Chernozhukov, Hansen and Kozbur (2016) <doi:10.1080/07350015.2015.1102733>.

Maintained by Joao Cruz. Last updated 2 months ago.

cpp

12 stars 5.56 score 10 scripts

bioc

methylclock:Methylclock - DNA methylation-based clocks

This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.

Maintained by Dolors Pelegri-Siso. Last updated 5 months ago.

dnamethylation biologicalquestion preprocessing statisticalmethod normalization cpp

39 stars 5.52 score 28 scripts

ropensci

mcbette:Model Comparison Using 'babette'

'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'mcbette' allows to do a Bayesian model comparison over some site and clock models, using 'babette' (<https://github.com/ropensci/babette/>).

Maintained by Richèl J.C. Bilderbeek. Last updated 8 months ago.

openjdk

7 stars 5.50 score 18 scripts

simon-smart88

shinyscholar:A Template for Creating Reproducible 'shiny' Applications

Create a skeleton 'shiny' application with create_template() that is reproducible, can be saved and meets academic standards for attribution. Forked from 'wallace'. Code is split into modules that are loaded and linked together automatically and each call one function. Guidance pages explain modules to users and flexible logging informs them of any errors. Options enable asynchronous operations, viewing of source code, interactive maps and data tables. Use to create complex analytical applications, following best practices in open science and software development. Includes functions for automating repetitive development tasks and an example application at run_shinyscholar() that requires install.packages("shinyscholar", dependencies = TRUE). A guide to developing applications can be found on the package website.

Maintained by Simon E. H. Smart. Last updated 7 days ago.

22 stars 5.40 score 5 scripts

darwin-eu-dev

PaRe:A Way to Perform Code Review or QA on Other Packages

Reviews other packages during code review by looking at their dependencies, code style, code complexity, and how internally defined functions interact with one another.

Maintained by Maarten van Kessel. Last updated 4 months ago.

3 stars 5.38 score 20 scripts

insightsengineering

verdepcheck:Check Package using Various Versions of Dependencies

Derive package dependencies from DESCRIPTION file using various strategies and run "R CMD CHECK" to validate package compatibility.

Maintained by Pawel Rucki. Last updated 6 months ago.

check devtools testing utils

7 stars 5.36 score 1 scripts

dynverse

babelwhale:Talking to 'Docker' and 'Singularity' Containers

Provides a unified interface to interact with 'docker' and 'singularity' containers. You can execute a command inside a container, mount a volume or copy a file.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

24 stars 5.33 score 15 scripts 2 dependents

mazamascience

MazamaTimeSeries:Core Functionality for Environmental Time Series

Utility functions for working with environmental time series data from known locations. The compact data model is structured as a list with two dataframes. A 'meta' dataframe contains spatial and measuring device metadata associated with deployments at known locations. A 'data' dataframe contains a 'datetime' column followed by columns of measurements associated with each "device-deployment". Ephemerides calculations are based on code originally found in NOAA's "Solar Calculator" <https://gml.noaa.gov/grad/solcalc/>.

Maintained by Jonathan Callahan. Last updated 1 years ago.

timeseries

5.27 score 62 scripts 1 dependents

ropensci

roreviewapi:Plumber API to report package structure and function

Plumber API to report package structure and function.

Maintained by Mark Padgham. Last updated 1 months ago.

4 stars 5.26 score

dynverse

lmds:Landmark Multi-Dimensional Scaling

A fast dimensionality reduction method scaleable to large numbers of samples. Landmark Multi-Dimensional Scaling (LMDS) is an extension of classical Torgerson MDS, but rather than calculating a complete distance matrix between all pairs of samples, only the distances between a set of landmarks and the samples are calculated.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

8 stars 5.26 score 10 scripts 3 dependents

stibu81

ibawds:Functions and Datasets for the Data Science Course at IBAW

A collection of useful functions and datasets for the Data Science Course at IBAW.

Maintained by Stefan Lanz. Last updated 10 days ago.

data-science-learning educational-resources

2 stars 5.24 score 8 scripts

pik-piam

modelstats:Run Analysis Tools

A collection of tools to analyze model runs.

Maintained by Anastasis Giannousakis. Last updated 14 days ago.

1 stars 5.19 score 2 scripts

feddelegrand7

batata:Managing Packages Removal and Installation

Allows the user to manage easily R packages removal and installation. It offers many functions to display installed packages according to specific dates and removes them if needed. The user is always prompted when running the removal functions in order to confirm the required action. It also provides functions that will install 'Github' starred R packages whether available on 'CRAN' or not.

Maintained by Mohamed El Fodil Ihaddaden. Last updated 4 years ago.

filesystem packages

28 stars 5.19 score 11 scripts

ncss-tech

soilReports:R Markdown Reports and Convenience Functions for Soil Survey

R package container and convenience functions for soil data summary, comparison, and evaluation reports used mainly by NRCS staff.

Maintained by Andrew Brown. Last updated 6 days ago.

nasis nrcs soil soil-survey usda

15 stars 5.17 score 41 scripts

ramikrispin

covid19sf:The Covid19 San Francisco Dataset

Provides a verity of summary tables of the Covid19 cases in San Francisco. Data source: San Francisco, Department of Public Health - Population Health Division <https://datasf.org/opendata/>.

Maintained by Rami Krispin. Last updated 2 years ago.

12 stars 5.16 score 12 scripts

larsenlab

hlaR:Tools for HLA Data

A streamlined tool for eplet analysis of donor and recipient HLA (human leukocyte antigen) mismatch. Messy, low-resolution HLA typing data is cleaned, and imputed to high-resolution using the NMDP (National Marrow Donor Program) haplotype reference database <https://haplostats.org/haplostats>. High resolution data is analyzed for overall or single antigen eplet mismatch using a reference table (currently supporting 'HLAMatchMaker' <http://www.epitopes.net> versions 2 and 3). Data can enter or exit the workflow at different points depending on the user's aims and initial data quality.

Maintained by Joan Zhang. Last updated 2 years ago.

7 stars 5.15 score 9 scripts

miriamesteve

GSSTDA:Progression Analysis of Disease with Survival using Topological Data Analysis

Mapper-based survival analysis with transcriptomics data is designed to carry out. Mapper-based survival analysis is a modification of Progression Analysis of Disease (PAD) where survival data is taken into account in the filtering function. More details in: J. Fores-Martos, B. Suay-Garcia, R. Bosch-Romeu, M.C. Sanfeliu-Alonso, A. Falco, J. Climent, "Progression Analysis of Disease with Survival (PAD-S) by SurvMap identifies different prognostic subgroups of breast cancer in a large combined set of transcriptomics and methylation studies" <doi:10.1101/2022.09.08.507080>.

Maintained by Miriam Esteve. Last updated 8 months ago.

2 stars 5.15 score 7 scripts

s-fleck

testthis:Utils and 'RStudio' Addins to Make Testing Even More Fun

Utility functions and 'RStudio' addins for writing, running and organizing automated tests. Integrates tightly with the packages 'testthat', 'devtools' and 'usethis'. Hotkeys can be assigned to the 'RStudio' addins for running tests in a single file or to switch between a source file and the associated test file. In addition, testthis provides function to manage and run tests in subdirectories of the test/testthat directory.

Maintained by Stefan Fleck. Last updated 3 years ago.

rstudio rstudio-addin rstudio-addins testing testthat

33 stars 5.12 score 20 scripts

yanrong-stacy-song

creditr:Credit Default Swaps

Price credit default swaps using 'C' code from the International Swaps and Derivatives Association CDS Standard Model. See <https://www.cdsmodel.com/cdsmodel/documentation.html> for more information about the model and <https://www.cdsmodel.com/cdsmodel/cds-disclaimer.html> for license details for the 'C' code.

Maintained by Yanrong Song. Last updated 8 days ago.

5.05 score 32 scripts

dieghernan

pkgdev:Helpers to Develop a Package using GitHub Actions

A small set of functions that takes advantage of GitHub Actions for making your life easier as a R package developer. This package is primarily intended for personal use, however feel free to use it (at your own risk :)).

Maintained by Diego Hernangómez. Last updated 7 days ago.

developer-tools experimental github-actions

4 stars 5.00 score 7 scripts

qile0317

FastUtils:Fast, Readable Utility Functions

A wide variety of tools for general data analysis, wrangling, spelling, statistics, visualizations, package development, and more. All functions have vectorized implementations whenever possible. Exported names are designed to be readable, with longer names possessing short aliases.

Maintained by Qile Yang. Last updated 4 months ago.

scientific-computing utilities utility cpp

2 stars 4.95 score 2 scripts

ryan-riggs

RivRetrieve:Retrieve Global River Gauge Data

Provides access to global river gauge data from a variety of national-level river agencies. The package interfaces with the national-level agency websites to provide access to river gauge locations, river discharge, and river stage. Currently, the package is available for the following countries: Australia, Brazil, Canada, Chile, France, Japan, South Africa, the United Kingdom, and the United States.

Maintained by Ryan Riggs. Last updated 3 months ago.

9 stars 4.95 score 7 scripts

openwashdata

washr:Publication Toolkit for Water, Sanitation and Hygiene (WASH) Data

A toolkit to set up an R data package in a consistent structure. Automates tasks like tidy data export, data dictionary documentation, README and website creation, and citation management.

Maintained by Colin Walder. Last updated 5 months ago.

2 stars 4.95 score 7 scripts

vincentguyader

shiny2docker:Generate Dockerfiles for 'Shiny' Applications

Automates the creation of Dockerfiles for deploying 'Shiny' applications. By integrating with 'renv' for dependency management and leveraging Docker-based solutions, it simplifies the process of containerizing 'Shiny' apps, ensuring reproducibility and consistency across different environments. Additionally, it facilitates the setup of CI/CD pipelines for building Docker images on both GitLab and GitHub.

Maintained by Vincent Guyader. Last updated 2 months ago.

8 stars 4.90 score

mazamascience

MazamaSpatialPlots:Thematic Plots for Mazama Spatial Datasets

A suite of convenience functions for generating US state and county thematic maps using datasets from the MazamaSpatialUtils package.

Maintained by Jonathan Callahan. Last updated 2 months ago.

4.84 score 23 scripts

analythium

deps:Dependency Management with 'roxygen'-Style Comments

Manage your source code dependencies by decorating your existing R code with special, 'roxygen'-style comments.

Maintained by Peter Solymos. Last updated 2 months ago.

dependencies packages reproducibility

31 stars 4.79 score 5 scripts

mkearney

pkgverse:Build a Meta-Package Universe

Build your own universe of packages similar to the 'tidyverse' package <https://tidyverse.org/> with this meta-package creator. Create a package-verse, or meta package, by supplying a custom name for the collection of packages and the vector of desired package names to include– and optionally supply a destination directory, an indicator of whether to keep the created package directory, and/or a vector of verbs implement via the 'usethis' <http://usethis.r-lib.org/> package.

Maintained by Michael Wayne Kearney. Last updated 6 years ago.

package-manager tidyverse

121 stars 4.78 score 6 scripts

seewe

dataCompare:A 'shiny' App to Compare Two Data Frames

A tool developed with the 'Golem' framework which provides an easier way to check cells differences between two data frames. The user provides two data frames for comparison, selects IDs variables identifying each row of input data, then clicks a button to perform the comparison. Several 'R' package functions are used to describe the data and perform the comparison in the server of the application. The main ones are comparedf() from 'arsenal' and skim() from 'skimr'. For more details see the description of comparedf() from the 'arsenal' package and that of skim() from the 'skimr' package.

Maintained by Sergio Ewane Ebouele. Last updated 3 months ago.

2 stars 4.78 score 4 scripts

jinkim3

exploratory:A Tool for Large-Scale Exploratory Analyses

Conduct numerous exploratory analyses in an instant with a point-and-click interface. With one simple command, this tool launches a Shiny App on the local machine. Drag and drop variables in a data set to categorize them as possible independent, dependent, moderating, or mediating variables. Then run dozens (or hundreds) of analyses instantly to uncover any statistically significant relationships among variables. Any relationship thus uncovered should be tested in follow-up studies. This tool is designed only to facilitate exploratory analyses and should NEVER be used for p-hacking. Many of the functions used in this package are previous versions of functions in the R Packages 'kim' and 'ezr'. Selected References: Chang et al. (2021) <https://CRAN.R-project.org/package=shiny>. Dowle et al. (2021) <https://CRAN.R-project.org/package=data.table>. Kim (2023) <https://jinkim.science/docs/kim.pdf>. Kim (2021) <doi:10.5281/zenodo.4619237>. Kim (2020) <https://CRAN.R-project.org/package=ezr>. Simmons et al. (2011) <doi:10.1177/0956797611417632> Tingley et al. (2019) <https://CRAN.R-project.org/package=mediation>. Wickham et al. (2020) <https://CRAN.R-project.org/package=ggplot2>.

Maintained by Jin Kim. Last updated 1 years ago.

5 stars 4.75 score 45 scripts

coursekata

coursekata:Packages and Functions for 'CourseKata' Courses

Easily install and load all packages and functions used in 'CourseKata' courses. Aid teaching with helper functions and augment generic functions to provide cohesion between the network of packages. Learn more about 'CourseKata' at <https://coursekata.org>.

Maintained by Adam Blake. Last updated 4 months ago.

4 stars 4.68 score 60 scripts

globalgov

manydata:A Portal for Global Governance Data

This is the core package for the many packages universe. It includes functions to help researchers work with and contribute to event datasets on global governance.

Maintained by James Hollway. Last updated 10 days ago.

data dataset

9 stars 4.65 score

bioc

methodical:Discovering genomic regions where methylation is strongly associated with transcriptional activity

DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework, lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites.

Maintained by Richard Heery. Last updated 2 months ago.

dnamethylation methylationarray transcription genomewideassociation software openjdk

4.65 score 14 scripts

techtonique

ahead:Time Series Forecasting with uncertainty quantification

Univariate and multivariate time series forecasting with uncertainty quantification.

Maintained by T. Moudiki. Last updated 1 months ago.

forecasting machine-learning predictive-modeling statistical-learning time-series time-series-forecasting uncertainty-quantification cpp

21 stars 4.63 score 51 scripts

sahirbhatnagar

eclust:Environment Based Clustering for Interpretable Predictive Models in High Dimensional Data

Companion package to the paper: An analytic approach for interpretable predictive models in high dimensional data, in the presence of interactions with exposures. Bhatnagar, Yang, Khundrakpam, Evans, Blanchette, Bouchard, Greenwood (2017) <DOI:10.1101/102475>. This package includes an algorithm for clustering high dimensional data that can be affected by an environmental factor.

Maintained by Sahir Rai Bhatnagar. Last updated 8 years ago.

2 stars 4.62 score 14 scripts

jinkim3

kim:A Toolkit for Behavioral Scientists

A collection of functions for analyzing data typically collected or used by behavioral scientists. Examples of the functions include a function that compares groups in a factorial experimental design, a function that conducts two-way analysis of variance (ANOVA), and a function that cleans a data set generated by Qualtrics surveys. Some of the functions will require installing additional package(s). Such packages and other references are cited within the section describing the relevant functions. Many functions in this package rely heavily on these two popular R packages: Dowle et al. (2021) <https://CRAN.R-project.org/package=data.table>. Wickham et al. (2021) <https://CRAN.R-project.org/package=ggplot2>.

Maintained by Jin Kim. Last updated 1 months ago.

7 stars 4.62 score 3 scripts

pik-piam

reporttransport:Reporting package for edgeTransport

This package contains edgeTransport-specific routines to report model results. The main functionality is to generate transport reporting variables in MIF format from a given edgeTransport model run folder or REMIND input data.

Maintained by Johanna Hoppe. Last updated 2 months ago.

4.60 score 9 scripts 3 dependents

inbo

INBOmd:Markdown Templates for INBO

Several templates to generate reports, presentations and posters.

Maintained by Thierry Onkelinx. Last updated 1 years ago.

bookdown rmarkdown xelatex

12 stars 4.52 score 11 scripts

learnitr

learnitdown:R Markdown, Bookdown and Learnr Additions for Learning Material

Extension to R Markdown, Bookdown and Learnr for building better learning and e-learning material: H5P integration, course-contextual divs, differed loading of Shiny and learnr applications, and much more ...

Maintained by Philippe Grosjean. Last updated 7 months ago.

bookdown learning-resources r-markdown teaching-materials

13 stars 4.49 score 16 scripts

pik-piam

piamValidation:Validation Tools for PIK-PIAM

The piamValidation package provides validation tools for the Potsdam Integrated Assessment Modelling environment.

Maintained by Pascal Weigmann. Last updated 4 days ago.

1 stars 4.49 score 13 scripts

r4epi

sitrep:Report templates and helper functions for applied epidemiology

Report templates and helper functions for applied epidemiology.

Maintained by Alexander Spina. Last updated 25 days ago.

epidemiology msf outbreaks report-generator

41 stars 4.46 score 9 scripts

certara

Certara.R:Easily Install Pharmacometric Packages and Shiny Applications Developed by Certara

A convenient set of wrapper functions to install pharmacometric packages and Shiny applications developed by Certara PMX and Integrated Drug Development (iDD). The functions ensure the successful installation of packages from non-standard repositories.

Maintained by James Craig. Last updated 5 months ago.

pharmacometrics r-pkg

14 stars 4.45 score 2 scripts

hubverse-org

hubDevs:Utilities for Creating and Standardising Hubverse Packages

What the package does (one paragraph).

Maintained by Anna Krystalli. Last updated 3 months ago.

hubverse

4.43 score 3 scripts

setempler

miscset:Miscellaneous Tools Set

A collection of miscellaneous methods to simplify various tasks, including plotting, data.frame and matrix transformations, environment functions, regular expression methods, and string and logical operations, as well as numerical and statistical tools. Most of the methods are simple but useful wrappers of common base R functions, which extend S3 generics or provide default values for important parameters.

Maintained by Sven E. Templer. Last updated 8 years ago.

miscellaneous cpp

1 stars 4.40 score 50 scripts

annechao

MF.beta4:Measuring Ecosystem Multi-Functionality and Its Decomposition

Provide simple functions to (i) compute a class of multi-functionality measures for a single ecosystem for given function weights, (ii) decompose gamma multi-functionality for pairs of ecosystems and K ecosystems (K can be greater than 2) into a within-ecosystem component (alpha multi-functionality) and an among-ecosystem component (beta multi-functionality). In each case, the correlation between functions can be corrected for. Based on biodiversity and ecosystem function data, this software also facilitates graphics for assessing biodiversity-ecosystem functioning relationships across scales.

Maintained by Anne Chao. Last updated 4 months ago.

4.40 score 3 scripts

michbur

AmpGram:Prediction of Antimicrobial Peptides

Predicts antimicrobial peptides using random forests trained on the n-gram encoded peptides (10.3390/ijms21124310). The implemented algorithm can be accessed from both the command line and shiny-based GUI. The AmpGram model is too large for CRAN and it has to be downloaded separately from the repository: <https://github.com/michbur/AmpGramModel>.

Maintained by Michal Burdukiewicz. Last updated 3 years ago.

4 stars 4.38 score 5 scripts

helske

changer:Change R Package Name

Changing the name of an existing R package is annoying but common task especially in the early stages of package development. This package (mostly) automates this task.

Maintained by Jouni Helske. Last updated 3 years ago.

47 stars 4.37 score 2 scripts

rmi-pacta

pacta.data.preparation:Prepare Data for PACTA for Investors

This package provides tools to prepare input datasets to be run in the PACTA_analysis tool.

Maintained by CJ Yetman. Last updated 5 months ago.

climate-change pacta pactaverse sustainable-finance

1 stars 4.36 score 11 scripts 1 dependents

dipterix

ravedash:Dashboard System for Reproducible Visualization of 'iEEG'

Dashboard system to display the analysis results produced by 'RAVE' (Magnotti J.F., Wang Z., Beauchamp M.S. (2020), Reproducible analysis and visualizations of 'iEEG' <doi:10.1016/j.neuroimage.2020.117341>). Provides infrastructure to integrate customized analysis pipelines into dashboard modules, including file structures, front-end widgets, and event handlers.

Maintained by Zhengjia Wang. Last updated 5 months ago.

1 stars 4.35 score 45 scripts

kserkcho

SCEM:Splitting-Coalescence-Estimation Method

We introduce improved methods for statistically assessing birth seasonality and intra-annual variation. The first method we propose is a new idea that uses a nonparametric clustering procedure to group individuals with similar time series data and estimate birth seasonality based on the clusters. One can use the function SCEM() to implement this method. The second method estimates input parameters for use with a previously-developed parametric approach (Tornero et al., 2013). The relevant code for this approach is makeFits_OLS(), while makeFits_initial() is the code to implement the same method but with given initial conditions for two parameters. The latter can be used to show the disadvantage of the existing approach. One can use the function makeFits() to generate parametric birth seasonality estimates using either initialization. Detailed description can be found here: Chazin Hannah, Soudeep Deb, Joshua Falk, and Arun Srinivasan. (2019) "New Statistical Approaches to Intra-Individual Isotopic Analysis and Modeling Birth Seasonality in Studies of Herd Animals." <doi:10.1111/arcm.12432>.

Maintained by Kyung Serk Cho. Last updated 4 years ago.

scem

4.30 score 3 scripts

bioc

protGear:Protein Micro Array Data Management and Interactive Visualization

A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.

Maintained by Kennedy Mwai. Last updated 5 months ago.

microarray onechannel preprocessing biomedicalinformatics proteomics batcheffect normalization bayesian clustering regression systemsbiology immunooncology background-correction microarray-data normalisation proteomics-data shiny shinydashboard

1 stars 4.30 score 6 scripts

bioc

oppti:Outlier Protein and Phosphosite Target Identifier

The aim of oppti is to analyze protein (and phosphosite) expressions to find outlying markers for each sample in the given cohort(s) for the discovery of personalized actionable targets.

Maintained by Abdulkadir Elmas. Last updated 5 months ago.

proteomics regression differentialexpression biomedicalinformatics genetarget geneexpression network

2 stars 4.30 score 2 scripts

green-striped-gecko

dartRverse:Install and Load the 'dartRverse' Suits of Packages

Provides a single function that supports the installation of all packages belonging to the 'dartRverse'. The 'dartRverse' is a set of packages that work together to analyse SNP (single nuclear polymorphism) data. All packages aim to have a similar 'look and feel' and are based on the same type of data structure ('genlight'), with additional metadata for loci and individuals (samples). For more information visit the 'GitHub' pages <https://github.com/green-striped-gecko/dartRverse>.

Maintained by Bernd Gruber. Last updated 18 days ago.

2 stars 4.27 score 47 scripts

dynverse

dyndimred:Dimensionality Reduction Methods in a Common Format

Provides a common interface for applying dimensionality reduction methods, such as Principal Component Analysis ('PCA'), Independent Component Analysis ('ICA'), diffusion maps, Locally-Linear Embedding ('LLE'), t-distributed Stochastic Neighbor Embedding ('t-SNE'), and Uniform Manifold Approximation and Projection ('UMAP'). Has built-in support for sparse matrices.

Maintained by Robrecht Cannoodt. Last updated 4 years ago.

7 stars 4.21 score 23 scripts

milesmcbain

capsule:A streamlined inversion of `renv`

A `capsule` is a stable local package library that you consciously choose to execute code within. Think of it as representing 'production', while your normal interactive R session represents 'development'.

Maintained by Miles McBain. Last updated 27 days ago.

156 stars 4.19 score 5 scripts

ingorohlfing

qcapower:Estimate Power and Required Sample Size in QCA

Researchers working with Qualitative Comparative Analysis (QCA) can use the package to estimate power of a sufficient term using permutation tests. A term can be anything: A condition, conjunction or disjunction of any combination of these. The package further allows users to plot the estimation results and to estimate the number of cases required to achieve a certain level of power, given a prespecified null and alternative hypothesis. Reference for the article introducing power estimation for QCA is: Rohlfing, Ingo (2018) <doi:10.1017/pan.2017.30> (ungated version: <doi:10.17605/OSF.IO/PC4DF>).

Maintained by Ingo Rohlfing. Last updated 5 years ago.

3 stars 4.18 score 7 scripts

marce10

sketchy:Create Custom Research Compendiums

Provides functions to create and manage research compendiums for data analysis. Research compendiums are a standard and intuitive folder structure for organizing the digital materials of a research project, which can significantly improve reproducibility. The package offers several compendium structure options that fit different research project as well as the ability of duplicating the folder structure of existing projects or implementing custom structures. It also simplifies the use of version control.

Maintained by Marcelo Araya-Salas. Last updated 4 months ago.

compendium research

3 stars 4.16 score 12 scripts

bioc

BUMHMM:Computational pipeline for computing probability of modification from structure probing experiment data

This is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a "drop-off rate" for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of variability in drop-off rate observed by chance and LDRs between treatment and control replicates gets compared to this distribution. Resulting empirical p-values (probability of being "drawn" from the null distribution) are used as observations in a Hidden Markov Model with a Beta-Uniform Mixture model used as an emission model. The resulting posterior probabilities indicate the probability of a nucleotide of having being modified in a structure probing experiment.

Maintained by Alina Selega. Last updated 5 months ago.

immunooncology geneticvariability transcription geneexpression generegulation coverage genetics structuralprediction transcriptomics bayesian classification featureextraction hiddenmarkovmodel regression rnaseq sequencing

4.15 score 14 scripts

globeandmail

upstartr:Utilities Powering the Globe and Mail's Data Journalism Template

Core functions necessary for using The Globe and Mail's R data journalism template, 'startr', along with utilities for day-to-day data journalism tasks, such as reading and writing files, producing graphics and cleaning up datasets.

Maintained by Tom Cardoso. Last updated 1 years ago.

data data-analysis data-journalism data-visualization journalism news

6 stars 4.14 score 46 scripts

inbo

protocolhelper:Helper Functions to Manage Protocols

Helper functions to manage INBO protocols.

Maintained by Hans Van Calster. Last updated 12 days ago.

5 stars 4.09 score 55 scripts

covid19r

covid19swiss:COVID-19 Cases in Switzerland and Principality of Liechtenstein

Provides a daily summary of the Coronavirus (COVID-19) cases in Switzerland cantons and Principality of Liechtenstein. Data source: Specialist Unit for Open Government Data Canton of Zurich <https://www.zh.ch/de/politik-staat/opendata.html>.

Maintained by Rami Krispin. Last updated 4 years ago.

4.00 score 8 scripts

marcellgranat

currr:Apply Mapping Functions in Frequent Saving

Implementations of the family of map() functions with frequent saving of the intermediate results. The contained functions let you start the evaluation of the iterations where you stopped (reading the already evaluated ones from cache), and work with the currently evaluated iterations while remaining ones are running in a background job. Parallel computing is also easier with the workers parameter.

Maintained by Marcell Granat. Last updated 7 months ago.

checkpoints parallel-computing purrr

20 stars 4.00 score 7 scripts

bioc

rifiComparative:'rifiComparative' compares the output of rifi from two different conditions.

'rifiComparative' is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.

Maintained by Loubna Youssar. Last updated 5 months ago.

rnaseq differentialexpression generegulation transcriptomics microarray software

4.00 score

dynverse

dynparam:Creating Meta-Information for Parameters

Provides tools for describing parameters of algorithms in an abstract way. Description can include an id, a description, a domain (range or list of values), and a default value. 'dynparam' can also convert parameter sets to a 'ParamHelpers' format, in order to be able to use 'dynparam' in conjunction with 'mlrMBO'.

Maintained by Robrecht Cannoodt. Last updated 6 years ago.

2 stars 3.95 score 15 scripts 2 dependents

repboxr

repboxDB:Functions for exported repbox data

Functions for exported repbox data

Maintained by Sebastian Kranz. Last updated 4 months ago.

3.91 score 8 scripts 9 dependents

biogenies

CancerGram:Prediction of Anticancer Peptides

Predicts anticancer peptides using random forests trained on the n-gram encoded peptides. The implemented algorithm can be accessed from both the command line and shiny-based GUI. The CancerGram model is too large for CRAN and it has to be downloaded separately from the repository: <https://github.com/BioGenies/CancerGramModel>. For more information see: Burdukiewicz et al. (2020) <doi:10.3390/pharmaceutics12111045>.

Maintained by Michal Burdukiewicz. Last updated 4 years ago.

anticancer-peptides bioinformatics k-mer n-gram peptide-identification random-forests

4 stars 3.90 score 3 scripts

wch

bisectr:Tools to Find Bad Commits with 'git bisect'

Tools to find bad commits with git bisect. See https://github.com/wch/bisectr for examples and test script templates.

Maintained by Winston Chang. Last updated 10 years ago.

16 stars 3.90 score 2 scripts

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.

cpp

1 stars 3.90 score 16 scripts

mrcaseb

personalr:Automated Personal Package Setup

Functions to setup a personal R package that attaches given libraries and exports personal helper functions.

Maintained by Sebastian Carl. Last updated 3 years ago.

13 stars 3.81 score 1 scripts

changwoolim

executablePackeR:Make 'shiny' App to Executable Program

Make your 'shiny' application as executable program. Users do not need to install 'R' and 'shiny' on their system.

Maintained by Changwoo Lim. Last updated 1 years ago.

11 stars 3.74 score 2 scripts

rmi-pacta

pactaverse:Easily Install and Load the 'PACTA-verse'

The 'pactaverse' is a set of packages that work to help R users implement various functionality related to the PACTA open source project.

Maintained by Jackson Hoffart. Last updated 4 months ago.

6 stars 3.73 score 3 scripts

jimhester

autoinst:Auto Install Packages

Automatically install packages when they are missing.

Maintained by Jim Hester. Last updated 7 years ago.

53 stars 3.72 score

pik-piam

mredgebuildings:Prepare data to be used by the EDGE-Buildings model

Prepare data to be used by the EDGE-Buildings model.

Maintained by Robin Hasse. Last updated 17 days ago.

3.72 score

repboxr

repboxReg:Repbox module for analysing regressions

Repbox module for analysing regressions

Maintained by Sebastian Kranz. Last updated 2 months ago.

3.71 score 6 scripts 2 dependents

kelliejarcher

ordinalbayes:Bayesian Ordinal Regression for High-Dimensional Data

Provides a function for fitting various penalized Bayesian cumulative link ordinal response models when the number of parameters exceeds the sample size. These models have been described in Zhang and Archer (2021) <doi:10.1186/s12859-021-04432-w>.

Maintained by Kellie J. Archer. Last updated 3 years ago.

jags cpp

1 stars 3.70 score 1 scripts

carlosyanez

just.install:Very Simple Function to Install Packages without Attaching

Install packages without attaching them. If a package it is already installed, it will be skipped.

Maintained by Carlos Yanez Santibanez. Last updated 3 years ago.

1 stars 3.70 score

drordas

D2MCS:Data Driving Multiple Classifier System

Provides a novel framework to able to automatically develop and deploy an accurate Multiple Classifier System based on the feature-clustering distribution achieved from an input dataset. 'D2MCS' was developed focused on four main aspects: (i) the ability to determine an effective method to evaluate the independence of features, (ii) the identification of the optimal number of feature clusters, (iii) the training and tuning of ML models and (iv) the execution of voting schemes to combine the outputs of each classifier comprising the Multiple Classifier System.

Maintained by Miguel Ferreiro-Díaz. Last updated 3 years ago.

openjdk

3.70 score

fvafrcu

packager:Create, Build and Maintain Packages

Helper functions for package creation, building and maintenance. Designed to work with a build system such as 'GNU make' or package 'fakemake' to help you to conditionally work through the stages of package development (such as spell checking, linting, testing, before building and checking a package).

Maintained by Andreas Dominik Cullmann. Last updated 1 years ago.

3.70 score 2 scripts

vasileioskarapoulios

LDNN:Longitudinal Data Neural Network

This is a Neural Network regression model implementation using 'Keras', consisting of 10 Long Short-Term Memory layers that are fully connected along with the rest of the inputs.

Maintained by Vasileios Karapoulios. Last updated 4 years ago.

3.70 score 6 scripts

sigbertklinke

smvgraph:Visualization and Clustering of Data in a Shiny App

Various visualisations of univariate and multivariate graphs (e.g. mosaic diagram, scatterplot matrix, Andrews curves, parallel coordinate diagram, radar diagram and Chernoff plots) as well as clustering methods (e.g. k-means, agglomerative, EM clustering and DBSCAN) are implemented as a Shiny app. The app allows interactive changes, e.g. of the order of variables. It is intended for use in teaching.

Maintained by Sigbert Klinke. Last updated 2 years ago.

3.70 score

joundso

requiRements:Helper Package to Install Packages for R

Helper function to install packages for R using an external 'requirements.txt' or a string containing diverse packages from several resources like Github or CRAN.

Maintained by Jonathan M. Mang. Last updated 2 years ago.

install requirements

9 stars 3.65 score 7 scripts

anthonynorth

using:Add version constraints to library() calls

Add version constraints and remote git repositories to library() calls. In interactive mode the user is prompted to install.

Maintained by Anthony North. Last updated 5 years ago.

28 stars 3.62 score 5 scripts 1 dependents

thinkr-open

testdown:'testhat' Results to Bookdown

Turn your 'testthat' results a Bookdown.

Maintained by Colin Fay. Last updated 2 years ago.

27 stars 3.61 score 3 scripts

melodyaowen

crt2power:Designing Cluster-Randomized Trials with Two Continuous Co-Primary Outcomes

Provides methods for powering cluster-randomized trials with two continuous co-primary outcomes using five key design techniques. Includes functions for calculating required sample size and statistical power. For more details on methodology, see Owen et al. (2025) <doi:10.1002/sim.70015>, Yang et al. (2022) <doi:10.1111/biom.13692>, Pocock et al. (1987) <doi:10.2307/2531989>, Vickerstaff et al. (2019) <doi:10.1186/s12874-019-0754-4>, and Li et al. (2020) <doi:10.1111/biom.13212>.

Maintained by Melody Owen. Last updated 17 days ago.

3.60 score 2 scripts

harrison4192

TidyConsultant:Tidy Consultant Universe

Loads the 5 packages in the Tidy Consultant Universe. This collection of packages is useful for anyone doing data science, data analysis, or quantitative consulting. The functions in these packages range from data cleaning, data validation, data binning, statistical modeling, and file exporting.

Maintained by Harrison Tietze. Last updated 10 months ago.

8 stars 3.60 score 2 scripts

repboxr

repboxHtml:HTML reports for repbox

HTML reports for repbox

Maintained by Sebastian Kranz. Last updated 2 months ago.

3.59 score 10 scripts 2 dependents

conjugateprior

cbn:Tools and replication materials for Caliskan, Bryson, and Narayanan (2017)

This package allows users to replicate the analysis in the paper and also provides general purpose tools for working with a large word vector file and comparing groups of words with permutation statistics from the original paper. Alternative bootstrapped versions with confidence intervals are also available.

Maintained by Will Lowe. Last updated 6 years ago.

cpp

2 stars 3.48 score 6 scripts

jumpingrivers

inteRgrate:Opinionated Package Coding Styles

A set of functions to enforce styling in functions. This package would typically be used in with a CI platform, such as GitHub and GitLab.

Maintained by Jumping Rivers. Last updated 3 years ago.

ci gitlab-ci travis-ci

20 stars 3.48 score 6 scripts

jfwambaugh

invivoPKfit:Fits Toxicokinetic Models to In Vivo PK Data Sets

Takes in vivo toxicokinetic concentration-time data and fits parameters of 1-compartment and 2-compartment models for each chemical. These methods are described in detail in "Informatics for Toxicokinetics" (submitted).

Maintained by John Wambaugh. Last updated 7 days ago.

3.48 score 4 scripts

achateigner

anyLib:Install and Load Any Package from CRAN, Bioconductor or Github

Made to make your life simpler with packages, by installing and loading a list of packages, whether they are on CRAN, Bioconductor or github. For github, if you do not have the full path, with the maintainer name in it (e.g. "achateigner/topReviGO"), it will be able to load it but not to install it.

Maintained by Aurelien Chateigner. Last updated 6 years ago.

3 stars 3.48 score 7 scripts

fastgitorg

fgitR:Using 'FastGit' to Accelerate the Access to 'GitHub'

'FastGit' <https://doc.fastgit.org/> works like a mirror of 'GitHub' to make significant acceleration. 'fgitR' is a package to do git operation with 'FastGit' automatically.

Maintained by Han Chen. Last updated 3 years ago.

6 stars 3.48 score 4 scripts

ifpri

GFSir:Global Food Security analysis using IMPACT model and R

Global Food Security analysis using IMPACT model and R.

Maintained by Abhijeet Mishra. Last updated 6 days ago.

3.40 score 1 scripts

repboxr

repboxRun:Run repbox analyses

Run repbox analyses

Maintained by Sebastian Kranz. Last updated 2 months ago.

3.36 score 11 scripts 1 dependents

mikelkou

ucie:Mapping 3D Data into CIELab Color Space

Returns a data frame with the names of the input data points and hex colors (or CIELab coordinates). Data can be mapped to colors for use in data visualization. It optimally maps data points into a polygon that represents the CIELab colour space. Since Euclidean distance approximates relative perceptual differences in CIELab color space, the result is a color encoding that aims to capture much of the structure of the original data.

Maintained by Mikaela Koutrouli. Last updated 2 years ago.

4 stars 3.30 score 6 scripts

ehmarwan

Elja:Linear, Logistic and Generalized Linear Models Regressions for the EnvWAS/EWAS Approach

Tool for Environment-Wide Association Studies (EnvWAS / EWAS) which are repeated analysis. It includes three functions. One function for linear regression, a second for logistic regression and a last one for generalized linear models.

Maintained by Marwan El Homsi. Last updated 2 years ago.

2 stars 3.30 score 2 scripts

dcauseur

ERP:Significance Analysis of Event-Related Potentials Data

Functions for signal detection and identification designed for Event-Related Potentials (ERP) data in a linear model framework. The functional F-test proposed in Causeur, Sheu, Perthame, Rufini (2018, submitted) for analysis of variance issues in ERP designs is implemented for signal detection (tests for mean difference among groups of curves in One-way ANOVA designs for example). Once an experimental effect is declared significant, identification of significant intervals is achieved by the multiple testing procedures reviewed and compared in Sheu, Perthame, Lee and Causeur (2016, <DOI:10.1214/15-AOAS888>). Some of the methods gathered in the package are the classical FDR- and FWER-controlling procedures, also available using function p.adjust. The package also implements the Guthrie-Buchwald procedure (Guthrie and Buchwald, 1991 <DOI:10.1111/j.1469-8986.1991.tb00417.x>), which accounts for the auto-correlation among t-tests to control erroneous detection of short intervals. The Adaptive Factor-Adjustment method is an extension of the method described in Causeur, Chu, Hsieh and Sheu (2012, <DOI:10.3758/s13428-012-0230-0>). It assumes a factor model for the correlation among tests and combines adaptively the estimation of the signal and the updating of the dependence modelling (see Sheu et al., 2016, <DOI:10.1214/15-AOAS888> for further details).

Maintained by David Causeur. Last updated 5 years ago.

3.30 score 20 scripts

natverse

natmanager:Install the 'Natverse' Packages from Scratch

Provides streamlined installation for packages from the 'natverse', a suite of R packages for computational neuroanatomy built on top of the 'nat' 'NeuroAnatomy Toolbox' package. Installation of the complete 'natverse' suite requires a 'GitHub' user account and personal access token 'GITHUB_PAT'. 'natmanager' will help the end user set this up if necessary.

Maintained by Gregory Jefferis. Last updated 8 months ago.

4 stars 3.30 score 1 scripts

bioc

Rmmquant:RNA-Seq multi-mapping Reads Quantification Tool

RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.

Maintained by Zytnicki Matthias. Last updated 5 months ago.

geneexpression transcription zlib cpp

3.30 score 5 scripts

repboxr

repboxMap:Mapping information from article and run supplement. Mainly (regression) tables.

This package should use as input only information stored in regdb tables.

Maintained by Sebastian Kranz. Last updated 2 months ago.

3.26 score 1 scripts 2 dependents

indenkun

readme2vignette:Convert README to Vignette During Package Installation

Convert README.md to vignettes when installing packages without vignettes.

Maintained by Mao Kobayashi. Last updated 9 months ago.

3.18 score

dipterix

ravepipeline:Reproducible Pipeline Infrastructure for Neuroscience

Defines the underlying pipeline structure for reproducible neuroscience, adopted by 'RAVE' (reproducible analysis and visualization of intracranial electroencephalography); provides high-level class definition to build, compile, set, execute, and share analysis pipelines. Both R and 'Python' are supported, with 'Markdown' and 'shiny' dashboard templates for extending and building customized pipelines. See the full documentations at <https://rave.wiki>; to cite us, check out our paper by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>), or run citation("ravepipeline") for details.

Maintained by Zhengjia Wang. Last updated 14 days ago.

3.18 score

torstax

amregtest:Runs Allelematch Regression Tests

Automates regression testing of package 'allelematch'. Over 2500 tests covers all functions in 'allelematch', reproduces the examples from the documentation and includes negative tests. The implementation is based on 'testthat'.

Maintained by Torvald Staxler. Last updated 12 months ago.

3.18 score 3 scripts

ifpri

DOORMAT:Data processor for IMPACT model (Data prOcessor fOR iMpAcT)

Data processor for IMPACT model.

Maintained by Abhijeet Mishra. Last updated 10 months ago.

3.18 score 5 dependents

curycu

valuemap:Making Choropleth Map

You can easily visualize your 'sf' polygons or data.frame with h3 address. While 'leaflet' package is too raw for data analysis, this package can save data analysts' efforts & time with pre-set visualize options.

Maintained by Huncheol Ha. Last updated 2 years ago.

geospatial leaflet sf

3 stars 3.18 score 5 scripts

coreofscience

margaret:Scientometric Analysis Minciencias

The target of 'margaret' is help to extract data from Minciencias to analyze scientific production in Colombia.

Maintained by Bryan Arias. Last updated 2 years ago.

3 stars 3.18 score 4 scripts

mrc-ide

provisionr:Provision a Library

Provision a set of packages into a new library, possibly for use on a different architecture.

Maintained by Rich FitzJohn. Last updated 5 years ago.

cluster infrastructure

27 stars 3.13 score 1 scripts

inqs909

csucistats:CSU Channel Islands R Tools

An R package containing functions for statistics courses at CSUCI.

Maintained by Isaac Quintanilla Salinas. Last updated 7 days ago.

3.02 score 14 scripts

hughjonesd

apicheck:Explore the Historical API of R Packages

Check when functions were introduced and/or APIs changed in packages, using the 'MRAN' service.

Maintained by David Hugh-Jones. Last updated 6 years ago.

21 stars 3.02 score 5 scripts

yhankcheng

psdr:Use Time Series to Generate and Compare Power Spectral Density

Functions that allow you to generate and compare power spectral density (PSD) plots given time series data. Fast Fourier Transform (FFT) is used to take a time series data, analyze the oscillations, and then output the frequencies of these oscillations in the time series in the form of a PSD plot.Thus given a time series, the dominant frequencies in the time series can be identified. Additional functions in this package allow the dominant frequencies of multiple groups of time series to be compared with each other. To see example usage with the main functions of this package, please visit this site: <https://yhhc2.github.io/psdr/articles/Introduction.html>. The mathematical operations used to generate the PSDs are described in these sites: <https://www.mathworks.com/help/matlab/ref/fft.html>. <https://www.mathworks.com/help/signal/ug/power-spectral-density-estimates-using-fft.html>.

Maintained by Yong-Han Hank Cheng. Last updated 4 years ago.

3.00 score 4 scripts

jimbrig

jimstools:Tools for R

What the package does (one paragraph).

Maintained by Jimmy Briggs. Last updated 3 years ago.

functions personal utility

2 stars 3.00 score 2 scripts

pakillo

safeinstall:Run some basic security checks before installing R packages from online repositories

Run some basic security checks before installing R packages from online repositories.

Maintained by Francisco Rodriguez-Sanchez. Last updated 6 years ago.

18 stars 2.95 score 6 scripts

zkamvar

beaverdown:An updated R Markdown thesis template for Oregon State University using the bookdown package

Using the bookdown package and LaTeX and Word thesis templates from Oregon State University, this package was derived from Chester Ismay's package "thesisdown"

Maintained by Zhian N. Kamvar. Last updated 8 years ago.

17 stars 2.93 score 2 scripts

mikejohnson51

climateR.catalogs:

A collection of tools for maniputatling hydrologic and hydraulic networks

Maintained by Mike Johnson. Last updated 1 years ago.

16 stars 2.90 score 1 scripts

burgette

OVtool:Omitted Variable Tool

This tool was designed to assess the sensitivity of research findings to omitted variables when estimating causal effects using propensity score (PS) weighting. This tool produces graphics and summary results that will enable a researcher to quantify the impact an omitted variable would have on their results. Burgette et al. (2021) describe the methodology behind the primary function in this package, ov_sim. The method is demonstrated in Griffin et al. (2020) <doi:10.1016/j.jsat.2020.108075>.

Maintained by Lane Burgette. Last updated 3 years ago.

2.78 score 12 scripts

iame-researchcenter

PFIM:Population Fisher Information Matrix

Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix. Methods used in the package refer to Mentré F, Mallet A, Baccar D (1997) <doi:10.1093/biomet/84.2.429>, Retout S, Comets E, Samson A, Mentré F (2007) <doi:10.1002/sim.2910>, Bazzoli C, Retout S, Mentré F (2009) <doi:10.1002/sim.3573>, Le Nagard H, Chao L, Tenaillon O (2011) <doi:10.1186/1471-2148-11-326>, Combes FP, Retout S, Frey N, Mentré F (2013) <doi:10.1007/s11095-013-1079-3> and Seurat J, Tang Y, Mentré F, Nguyen TT (2021) <doi:10.1016/j.cmpb.2021.106126>.

Maintained by Romain Leroux. Last updated 5 months ago.

2.78 score 9 scripts

repboxr

repboxCodeText:Extracting purely text based information from supplement code

Extracting purely text based information from supplement code

Maintained by Sebastian Kranz. Last updated 11 months ago.

2.78 score 1 scripts 2 dependents

terminological

ggrrr:Addressing Annoyances and Irritations

Visualisation hacks, tabular data helpers, fonts, caching, tidy data functions. It is an swiss army knife, jack of all trades.

Maintained by Robert Challen. Last updated 10 months ago.

1 stars 2.74 score 11 scripts

repboxr

repboxStata:Repbox analysis of stata scripts in reproduction packages

Repbox analysis of stata scripts in reproduction packages

Maintained by Sebastian Kranz. Last updated 2 months ago.

2.73 score 4 scripts 2 dependents

obrienjoey

spRingsteen:All Things Data and Springsteen

An R data package containing setlists from all Bruce Springsteen concerts over 1973-2021. Also includes all his song details such as lyrics and albums. Data extracted from: <http://brucebase.wikidot.com/>.

Maintained by Joey OBrien. Last updated 1 years ago.

2.70 score 1 scripts

chuxinyuan

ipkg:Install R Packages or Download File from GitHub via the Proxy Site

When you want to install R package or download file from GitHub, but you can't access GitHub, this package helps you install R packages or download file from GitHub via the proxy website <https://gh-proxy.com/> or <https://ghfast.top/>, which is in real-time sync with GitHub.

Maintained by Xinyuan Chu. Last updated 1 months ago.

2.70 score

kwb-r

kwb.package:Install / Unstall KWB Packages and Show Package Dependencies

This package contains some helper functions for (un-)installing KWB packages and for showing package dependencies. The function of main interest may be updateKwbPackages() that checks for the latest package version on KWB's server and installs the packages from there if required.

Maintained by Hauke Sonnenberg. Last updated 11 months ago.

package-installation

2.70 score 1 scripts

ifpri

KIRAN:Package for setting up Key IMPACT R-Archive Network suite of packages

Establishes the KIRAN suite of R based packages.

Maintained by Abhijeet Mishra. Last updated 2 years ago.

2.70 score

yaoxiangli

ShinyLink:'Shiny' Based Record Linkage Tool

A bridge is created between existing robust open-source record linkage algorithms and an urgently needed user-friendly platform that removes financial and technical barriers, setting a new standard for data interoperability in public health and bioinformatics. The 'fastLink' algorithms are used for matching. Ted Enamorado et al. (2019) <doi:10.1017/S0003055418000783>.

Maintained by Yaoxiang Li. Last updated 2 years ago.

2.70 score 6 scripts

ifpri

ARIA:App for IMPACT (App foR ImpAct)

App for IMPACT (App foR ImpAct).

Maintained by Abhijeet Mishra. Last updated 10 months ago.

2.70 score 6 scripts

soodoku

rdomains:Get the Category of Content Hosted by a Domain

Get the category of content hosted by a domain. Use Shallalist <http://shalla.de/>, Virustotal (which provides access to lots of services) <https://www.virustotal.com/>, Alexa <https://aws.amazon.com/awis/>, DMOZ <https://curlie.org/>, University Domain list <https://github.com/Hipo/university-domains-list> or validated machine learning classifiers based on Shallalist data to learn about the kind of content hosted by a domain.

Maintained by Gaurav Sood. Last updated 3 years ago.

2.70 score 7 scripts

vtshen

AHM:Additive Heredity Model: Method for the Mixture-of-Mixtures Experiments

An implementation of the additive heredity model for the mixture-of-mixtures experiments of Shen et al. (2019) in Technometrics <doi:10.1080/00401706.2019.1630010>. The additive heredity model considers an additive structure to inherently connect the major components with the minor components. The additive heredity model has a meaningful interpretation for the estimated model because of the hierarchical and heredity principles applied and the nonnegative garrote technique used for variable selection.

Maintained by Sumin Shen. Last updated 6 years ago.

2.70 score 2 scripts

mascotnum

templr:MASCOTNUM Algorithms Template Tools

Helper functions for MASCOTNUM algorithm template, for design of numerical experiments practice: algorithm template parser to support MASCOTNUM specification <https://www.gdr-mascotnum.fr/template.html>, 'ask & tell' decoupling injection (inspired by <https://search.r-project.org/CRAN/refmans/sensitivity/html/decoupling.html>) to use "crimped" algorithms (like uniroot(), optim(), ...) from outside R, basic template examples: Brent algorithm for 1 dim root finding and L-BFGS-B from base optim().

Maintained by Yann Richet. Last updated 2 years ago.

2.70 score 1 scripts

pik-piam

edgeTrpLib:Helper functions for EDGE transport calculations

This package is highly specialized and created solely to not duplicate helper functions.

Maintained by Alois Dirnaichner. Last updated 3 years ago.

2.54 score 5 scripts

stephenturner

Tverse:Meta package that installs my most commonly used packages

Meta package that installs my most commonly used packages.

Maintained by Stephen Turner. Last updated 7 months ago.

6 stars 2.48 score

kwb-r

kwb.abimo:R Package with Functions for Working with Water Balance Model ABIMO

R Package with functions for working with water balance bodel ABIMO https://www.stadtentwicklung.berlin.de/umwelt/umweltatlas/download/goedecke_et_al_abimo2019_doku.pdf).

Maintained by Andreas Matzinger. Last updated 1 years ago.

abimo project-amarex project-basar project-flusshygiene project-keys project-kuras project-ogre project-spur water-balance-model

2.48 score 1 dependents

repboxr

repboxR:Repbox for R code files in code supplements

Repbox for R code files in code supplements

Maintained by Sebastian Kranz. Last updated 1 years ago.

2.48 score 2 dependents

barryzee

NoviceDeveloperResources:Resources to Assist Novice Developers

Assist novice developers when preparing a single package or a set of integrated packages to submit to CRAN. Automate the following individual or batch processing: check local source packages; build local .tar.gz source files; install packages from local .tar.gz files; detect conflicts between function names in the environment.

Maintained by Barry Zeeberg. Last updated 11 months ago.

2.48 score 1 dependents

ices-tools-prod

fisheryO:Fisheries Overviews for ICES Advice

Functions that work with International Council for the Exploration of the Sea (ICES) web services and databases to collate, aggregate, and plot Fisheries Overview products.

Maintained by Scott Large. Last updated 7 years ago.

3 stars 2.45 score 19 scripts

cran

DCEtool:Efficient and Accessible Discrete Choice Experiments

Design, conduct and analyze 'DCEs' from a virtual interface in shiny. Reference: Perez-Troncoso, D. (2022) <https://github.com/danielpereztr/DCEtool>.

Maintained by Daniel Perez Troncoso. Last updated 2 years ago.

2 stars 2.30 score

barryzee

SherlockHolmes:Building a Concordance of Terms in a Series of Texts

Compute the frequency distribution of a search term in a series of texts. For example, Arthur Conan Doyle wrote a total of 60 Sherlock Holmes stories, comprised of 54 short stories and 4 longer novels. I wanted to test my own subjective impression that, in many of the stories, Sherlock Holmes' popularity was used as bait to induce the reader to read a story that is essentially not primarily a Sherlock Holmes story. I used the term "Holmes" as a search pattern, since Watson would frequently address him by name, or use his name to describe something that he was doing. My hypothesis is that the frequency distribution of the search pattern "Holmes" is a good proxy for the degree to which a story is or is not truly a Sherlock Holmes story. The results are presented in a manuscript that is available as a vignette and online at <https://barryzee.github.io/Concordance/index.html>.

Maintained by Barry Zeeberg. Last updated 2 years ago.

2.30 score