R-universe search: tools

pik-piam

madrat:May All Data be Reproducible and Transparent (MADRaT) *

Provides a framework which should improve reproducibility and transparency in data processing. It provides functionality such as automatic meta data creation and management, rudimentary quality management, data caching, work-flow management and data aggregation. * The title is a wish not a promise. By no means we expect this package to deliver everything what is needed to achieve full reproducibility and transparency, but we believe that it supports efforts in this direction.

Maintained by Jan Philipp Dietrich. Last updated 2 days ago.

44.0 match 15 stars 11.01 score 83 scripts 38 dependents

opengeos

whitebox:'WhiteboxTools' R Frontend

An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.

Maintained by Andrew Brown. Last updated 5 months ago.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

39.2 match 173 stars 9.65 score 203 scripts 2 dependents

paws-r

paws.developer.tools:'Amazon Web Services' Developer Tools Services

Interface to 'Amazon Web Services' developer tools services, including version control, continuous integration and deployment, and more <https://aws.amazon.com/products/developer-tools/>.

Maintained by Dyfan Jones. Last updated 3 days ago.

aws aws-sdk

38.9 match 332 stars 9.03 score 14 dependents

matteo21q

jomo:Multilevel Joint Modelling Multiple Imputation

Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) <doi:10.1002/9781119942283>. Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.

Maintained by Matteo Quartagno. Last updated 3 years ago.

36.4 match 3 stars 9.58 score 126 scripts 154 dependents

decisionpatterns

formula.tools:Programmatic Utilities for Manipulating Formulas, Expressions, Calls, Assignments and Other R Objects

These utilities facilitate the programmatic manipulations of formulas, expressions, calls, assignments and other R language objects. These objects all share the same structure: a left-hand side, operator and right-hand side. This packages provides methods for accessing and modifying this structures as well as extracting and replacing names and symbols from these objects.

Maintained by Christopher Brown. Last updated 7 years ago.

37.5 match 17 stars 8.89 score 236 scripts 79 dependents

predictiveecology

SpaDES.tools:Additional Tools for Developing Spatially Explicit Discrete Event Simulation (SpaDES) Models

Provides GIS and map utilities, plus additional modeling tools for developing cellular automata, dynamic raster models, and agent based models in 'SpaDES'. Included are various methods for spatial spreading, spatial agents, GIS operations, random map generation, and others. See '?SpaDES.tools' for an categorized overview of these additional tools. The suggested package 'NLMR' can be installed from the following repository: (<https://PredictiveEcology.r-universe.dev>).

Maintained by Alex M Chubaty. Last updated 4 months ago.

cpp

43.0 match 4 stars 7.55 score 52 scripts 6 dependents

bioc

sevenbridges:Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.

Maintained by Phil Webster. Last updated 5 months ago.

software dataimport thirdpartyclient api-client bioconductor bioinformatics cloud common-workflow-language sevenbridges

41.4 match 35 stars 7.40 score 24 scripts

decisionpatterns

operator.tools:Utilities for Working with R's Operators

Provides a collection of utilities that allow programming with R's operators. Routines allow classifying operators, translating to and from an operator and its underlying function, and inverting some operators (e.g. comparison operators), etc. All methods can be extended to custom infix operators.

Maintained by Christopher Brown. Last updated 7 years ago.

39.3 match 4 stars 7.26 score 23 scripts 81 dependents

forestgeo

fgeo.tool:Import and Manipulate 'ForestGEO' Data

To help you access, transform, analyze, and visualize 'ForestGEO' data, we developed a collection of R packages (<https://forestgeo.github.io/fgeo/>). This package, in particular, helps you to easily import, filter, and modify 'ForestGEO' data. To learn more about 'ForestGEO' visit <https://forestgeo.si.edu/>.

Maintained by Mauro Lepore. Last updated 3 years ago.

dynamics ecology fgeo forestgeo miscelaneas tools tree utils

47.5 match 2 stars 4.86 score 27 scripts 3 dependents

bioc

Mergeomics:Integrative network analysis of omics data

The Mergeomics pipeline serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts, 1) Marker set enrichment analysis (MSEA); 2) Weighted Key Driver Analysis (wKDA).

Maintained by Zeyneb Kurt. Last updated 5 months ago.

software

53.3 match 4.30 score 8 scripts

tidyverse

ellmer:Chat with Large Language Models

Chat with large language models from a range of providers including 'Claude' <https://claude.ai>, 'OpenAI' <https://chatgpt.com>, and more. Supports streaming, asynchronous calls, tool calling, and structured data extraction.

Maintained by Hadley Wickham. Last updated 9 hours ago.

17.2 match 391 stars 12.65 score 98 scripts 7 dependents

satijalab

Seurat:Tools for Single Cell Genomics

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Maintained by Paul Hoffman. Last updated 1 years ago.

human-cell-atlas single-cell-genomics single-cell-rna-seq cpp

11.2 match 2.4k stars 16.86 score 50k scripts 73 dependents

rundel

ghclass:Tools for Managing Classes on GitHub

Interface for the GitHub API that enables efficient management of courses on GitHub. It has a functionality for managing organizations, teams, repositories, and users on GitHub and helps automate most of the tedious and repetitive tasks around creating and distributing assignments.

Maintained by Colin Rundel. Last updated 1 months ago.

24.7 match 142 stars 7.32 score 70 scripts

pakillo

network.tools:Tools to Analyse and Visualise Bipartite Networks

Tools to analyse and visualise bipartite networks.

Maintained by Francisco Rodriguez-Sanchez. Last updated 9 months ago.

41.1 match 2 stars 4.18 score 8 scripts 1 dependents

stan-dev

rstantools:Tools for Developing R Packages Interfacing with 'Stan'

Provides various tools for developers of R packages interfacing with 'Stan' <https://mc-stan.org>, including functions to set up the required package structure, S3 generics and default methods to unify function naming across 'Stan'-based R packages, and vignettes with recommendations for developers.

Maintained by Jonah Gabry. Last updated 2 months ago.

bayesian-data-analysis bayesian-statistics developer-tools stan

12.7 match 50 stars 13.09 score 134 scripts 222 dependents

rstudio

pointblank:Data Validation and Organization of Metadata for Local and Remote Tables

Validate data in data frames, 'tibble' objects, 'Spark' 'DataFrames', and database tables. Validation pipelines can be made using easily-readable, consecutive validation steps. Upon execution of the validation plan, several reporting options are available. User-defined thresholds for failure rates allow for the determination of appropriate reporting actions. Many other workflows are available including an information management workflow, where the aim is to record, collect, and generate useful information on data tables.

Maintained by Richard Iannone. Last updated 9 days ago.

data-assertions data-checker data-dictionaries data-frames data-inference data-management data-profiler data-quality data-validation data-verification database-tables easy-to-understand reporting-tool schema-validation testing-tools yaml-configuration

15.0 match 932 stars 10.59 score 284 scripts

efinite

utile.tools:Summarize Data for Publication

Tools for formatting and summarizing data for outcomes research.

Maintained by Eric Finnesgard. Last updated 2 years ago.

38.1 match 5 stars 3.99 score 13 scripts 1 dependents

decisionpatterns

na.tools:Comprehensive Library for Working with Missing (NA) Values in Vectors

This comprehensive toolkit provide a consistent and extensible framework for working with missing values in vectors. The companion package 'tidyimpute' provides similar functionality for list-like and table-like structures). Functions exist for detection, removal, replacement, imputation, recollection, etc. of 'NAs'.

Maintained by Christopher Brown. Last updated 6 years ago.

37.5 match 2 stars 4.04 score 109 scripts

bioc

ChemmineR:Cheminformatics Toolkit for R

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.

Maintained by Thomas Girke. Last updated 5 months ago.

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics microtitreplateassay cellbasedassays visualization infrastructure dataimport clustering proteomics metabolomics cpp

15.3 match 14 stars 9.42 score 253 scripts 12 dependents

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.

13.3 match 466 stars 10.41 score 79 scripts 2 dependents

r-lib

pkgdown:Make Static HTML Documentation for a Package

Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.

Maintained by Hadley Wickham. Last updated 9 hours ago.

documentation-tool

7.5 match 734 stars 18.47 score 588 scripts 162 dependents

tidymodels

dials:Tools for Creating Tuning Parameter Values

Many models contain tuning parameters (i.e. parameters that cannot be directly estimated from the data). These tools can be used to define objects for creating, simulating, or validating values for such parameters.

Maintained by Hannah Frick. Last updated 29 days ago.

9.1 match 114 stars 14.22 score 426 scripts 52 dependents

r-lib

pkgbuild:Find Tools Needed to Build R Packages

Provides functions used to build R packages. Locates compilers needed to build R packages on various platforms and ensures the PATH is configured appropriately so R can use them.

Maintained by Gábor Csárdi. Last updated 1 months ago.

8.6 match 66 stars 13.90 score 133 scripts 869 dependents

bmcclintock

momentuHMM:Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models

Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, discrete- or continuous-time HMMs, continuous- or discrete-space movement models, approximate Langevin diffusion models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.

Maintained by Brett McClintock. Last updated 30 days ago.

openblas cpp

13.6 match 43 stars 8.47 score 162 scripts

statnmap

servers.tools:Extra Tools For Server Use

Use tools.

Maintained by Sebastien Rochette. Last updated 3 years ago.

41.4 match 2.70 score

bioc

Maaslin2:"Multivariable Association Discovery in Population-scale Meta-omics Studies"

MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. MaAsLin2 is the next generation of MaAsLin.

Maintained by Lauren McIver. Last updated 5 months ago.

metagenomics software microbiome normalization biobakery bioconductor differential-abundance-analysis false-discovery-rate multiple-covariates public repeated-measures tools

10.0 match 133 stars 11.03 score 532 scripts 3 dependents

usaid-oha-si

tameDP:Import targets and PLHIV data from COP Target Setting Tool (formerly Data Pack)

Import PSNUxIM targets and PLHIV data from COP Data Pack. The purpose is to make the data tidy and more usable than their current structure in the Excel data packs.

Maintained by Aaron Chafetz. Last updated 1 years ago.

22.0 match 1 stars 4.92 score 46 scripts

futureverse

future.tools:Tools for Working with Futures

Tools for Working with Futures.

Maintained by Henrik Bengtsson. Last updated 10 months ago.

parallel-computing parallel-programming

41.5 match 2 stars 2.60 score

eliocamp

metR:Tools for Easier Analysis of Meteorological Fields

Many useful functions and extensions for dealing with meteorological data in the tidy data framework. Extends 'ggplot2' for better plotting of scalar and vector fields and provides commonly used analysis methods in the atmospheric sciences.

Maintained by Elio Campitelli. Last updated 20 days ago.

atmospheric-science ggplot2 visualization

8.5 match 144 stars 12.19 score 1000 scripts 22 dependents

winvector

wrapr:Wrap R Tools for Debugging and Parametric Programming

Tools for writing and debugging R code. Provides: '%.>%' dot-pipe (an 'S3' configurable pipe), unpack/to (R style multiple assignment/return), 'build_frame()'/'draw_frame()' ('data.frame' example tools), 'qc()' (quoting concatenate), ':=' (named map builder), 'let()' (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by 'gtools::strmacro()' and 'base::bquote()'), and more.

Maintained by John Mount. Last updated 2 years ago.

9.2 match 137 stars 11.11 score 390 scripts 12 dependents

ropensci

babelquarto:Renders a Multilingual Quarto Book

Automate rendering and cross-linking of Quarto books following a prescribed structure.

Maintained by Maëlle Salmon. Last updated 1 months ago.

13.3 match 43 stars 7.52 score 23 scripts 1 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 5 days ago.

compliance-automation software-analysis software-checking

13.3 match 19 stars 7.13 score 29 scripts 1 dependents

satijalab

SeuratObject:Data Structures for Single Cell Data

Defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.

Maintained by Paul Hoffman. Last updated 1 years ago.

cpp

8.1 match 25 stars 11.69 score 1.2k scripts 88 dependents

ipd-tools

ipd:Inference on Predicted Data

Performs valid statistical inference on predicted data (IPD) using recent methods, where for a subset of the data, the outcomes have been predicted by an algorithm. Provides a wrapper function with specified defaults for the type of model and method to be used for estimation and inference. Further provides methods for tidying and summarizing results. Salerno et al., (2024) <doi:10.48550/arXiv.2410.09665>.

Maintained by Stephen Salerno. Last updated 2 months ago.

15.0 match 8 stars 6.13 score 5 scripts

matloff

regtools:Regression and Classification Tools

Tools for linear, nonlinear and nonparametric regression and classification. Novel graphical methods for assessment of parametric models using nonparametric methods. One vs. All and All vs. All multiclass classification, optional class probabilities adjustment. Nonparametric regression (k-NN) for general dimension, local-linear option. Nonlinear regression with Eickert-White method for dealing with heteroscedasticity. Utilities for converting time series to rectangular form. Utilities for conversion between factors and indicator variables. Some code related to "Statistical Regression and Classification: from Linear Models to Machine Learning", N. Matloff, 2017, CRC, ISBN 9781498710916.

Maintained by Norm Matloff. Last updated 2 months ago.

9.8 match 127 stars 9.39 score 48 scripts 3 dependents

ices-tools-prod

TAF:Transparent Assessment Framework for Reproducible Research

General framework to organize data, methods, and results used in reproducible scientific analyses. A TAF analysis consists of four scripts (data.R, model.R, output.R, report.R) that are run sequentially. Each script starts by reading files from a previous step and ends with writing out files for the next step. Convenience functions are provided to version control the required data and software, run analyses, clean residues from previous runs, manage files, manipulate tables, and produce figures. With a focus on stability and reproducible analyses, the TAF package comes with no dependencies. TAF forms a base layer for the 'icesTAF' package and other scientific applications.

Maintained by Arni Magnusson. Last updated 4 months ago.

13.3 match 3 stars 6.85 score 282 scripts 2 dependents

ropensci

pkgstats:Metrics of R Packages

Static code analyses for R packages using the external code-tagging libraries 'ctags' and 'gtags'. Static analyses enable packages to be analysed very quickly, generally a couple of seconds at most. The package also provides access to a database generating by applying the main function to the full 'CRAN' archive, enabling the statistical properties of any package to be compared with all other 'CRAN' packages.

Maintained by Mark Padgham. Last updated 18 days ago.

code-analysis code-statistics software-analysis cpp

13.3 match 17 stars 6.81 score 1 scripts 3 dependents

bioc

oligo:Preprocessing tools for oligonucleotide arrays

A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

Maintained by Benilton Carvalho. Last updated 7 days ago.

microarray onechannel twochannel preprocessing snp differentialexpression exonarray geneexpression dataimport zlib

8.6 match 3 stars 10.42 score 528 scripts 10 dependents

rstudio

reticulate:Interface to 'Python'

Interface to 'Python' modules, classes, and functions. When calling into 'Python', R data types are automatically converted to their equivalent 'Python' types. When values are returned from 'Python' to R they are converted back to R types. Compatible with all versions of 'Python' >= 2.7.

Maintained by Tomasz Kalinowski. Last updated 1 days ago.

cpp

4.3 match 1.7k stars 21.07 score 18k scripts 427 dependents

bioc

scviR:experimental inferface from R to scvi-tools

This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another vignette compares outputs of Chapter 12 of the OSCA book with analogous outputs based on totalVI quantifications. Future work will address other components of scvi-tools, with a focus on building understanding of probabilistic methods based on variational autoencoders.

Maintained by Vincent Carey. Last updated 5 months ago.

infrastructure singlecell dataimport bioconductor cite-seq scverse

16.0 match 6 stars 5.60 score 11 scripts

r-lib

testthat:Unit Testing for R

Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy to learn and use, and integrates with your existing 'workflow'.

Maintained by Hadley Wickham. Last updated 16 days ago.

unit-testing cpp

4.3 match 900 stars 20.97 score 74k scripts 465 dependents

eddelbuettel

drat:'Drat' R Archive Template

Creation and use of R Repositories via helper functions to insert packages into a repository, and to add repository information to the current R session. Two primary types of repositories are support: gh-pages at GitHub, as well as local repositories on either the same machine or a local network. Drat is a recursive acronym: Drat R Archive Template.

Maintained by Dirk Eddelbuettel. Last updated 3 months ago.

repository repository-tools

7.5 match 153 stars 11.72 score 112 scripts 11 dependents

dnychka

fields:Tools for Spatial Data

For curve, surface and function fitting with an emphasis on splines, spatial data, geostatistics, and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding the source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857, the National Center for Atmospheric Research, and Colorado School of Mines. See the Fields URL for a vignette on using this package and some background on spatial statistics.

Maintained by Douglas Nychka. Last updated 9 months ago.

fortran

7.0 match 15 stars 12.60 score 7.7k scripts 295 dependents

stan-dev

posterior:Tools for Working with Posterior Distributions

Provides useful tools for both users and developers of packages for fitting Bayesian models or working with output from Bayesian models. The primary goals of the package are to: (a) Efficiently convert between many different useful formats of draws (samples) from posterior or prior distributions. (b) Provide consistent methods for operations commonly performed on draws, for example, subsetting, binding, or mutating draws. (c) Provide various summaries of draws in convenient formats. (d) Provide lightweight implementations of state of the art posterior inference diagnostics. References: Vehtari et al. (2021) <doi:10.1214/20-BA1221>.

Maintained by Paul-Christian Bürkner. Last updated 10 days ago.

bayes bayesian mcmc

5.4 match 168 stars 16.13 score 3.3k scripts 342 dependents

ices-tools-prod

icesTAF:Functions to Support the ICES Transparent Assessment Framework

Functions to support the ICES Transparent Assessment Framework <https://taf.ices.dk> to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science.

Maintained by Colin Millar. Last updated 2 years ago.

13.3 match 5 stars 6.37 score 1.1k scripts 1 dependents

andrisignorell

DescTools:Tools for Descriptive Statistics

A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.

Maintained by Andri Signorell. Last updated 9 days ago.

fortran cpp

5.1 match 87 stars 16.68 score 7.7k scripts 99 dependents

ropensci

autotest:Automatic Package Testing

Automatic testing of R packages via a simple YAML schema.

Maintained by Mark Padgham. Last updated 5 months ago.

13.3 match 54 stars 6.31 score 25 scripts

ices-tools-prod

icesSAG:Stock Assessment Graphs Database Web Services

R interface to access the web services of the ICES Stock Assessment Graphs database <https://sg.ices.dk>.

Maintained by Colin Millar. Last updated 5 months ago.

13.3 match 11 stars 6.24 score 131 scripts 2 dependents

pakillo

taxonomy.tools:Tools to Work with Taxonomic Data

Tools to Work with Taxonomic Data.

Maintained by Francisco Rodriguez-Sanchez. Last updated 3 months ago.

41.3 match 2.00 score 3 scripts

ices-tools-prod

icesDatras:DATRAS Trawl Survey Database Web Services

R interface to access the web services of the ICES (International Council for the Exploration of the Sea) DATRAS trawl survey database <https://datras.ices.dk/WebServices/Webservices.aspx>.

Maintained by Colin Millar. Last updated 1 months ago.

13.3 match 12 stars 5.92 score 115 scripts

lydialucchesi

smallsets:Visual Documentation for Data Preprocessing

Data practitioners regularly use the 'R' and 'Python' programming languages to prepare data for analyses. Thus, they encode important data preprocessing decisions in 'R' and 'Python' code. The 'smallsets' package subsequently decodes these decisions into a Smallset Timeline, a static, compact visualisation of data preprocessing decisions (Lucchesi et al. (2022) <doi:10.1145/3531146.3533175>). The visualisation consists of small data snapshots of different preprocessing steps. The 'smallsets' package builds this visualisation from a user's dataset and preprocessing code located in an 'R', 'R Markdown', 'Python', or 'Jupyter Notebook' file. Users simply add structured comments with snapshot instructions to the preprocessing code. One optional feature in 'smallsets' requires installation of the 'Gurobi' optimisation software and 'gurobi' 'R' package, available from <https://www.gurobi.com>. More information regarding the optional feature and 'gurobi' installation can be found in the 'smallsets' vignette.

Maintained by Lydia R. Lucchesi. Last updated 2 months ago.

data-science data-visualization documentation-tool machine-learning preprocessing python visualization-tools

15.0 match 14 stars 5.19 score 11 scripts

rstudio

htmltools:Tools for HTML

Tools for HTML generation and output.

Maintained by Carson Sievert. Last updated 10 months ago.

4.4 match 218 stars 17.61 score 10k scripts 4.5k dependents

kbroman

qtl:Tools for Analyzing QTL Experiments

Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.

Maintained by Karl W Broman. Last updated 7 months ago.

openblas

6.0 match 80 stars 12.79 score 2.4k scripts 29 dependents

yulab-smu

tidytree:A Tidy Tool for Phylogenetic Tree Data Manipulation

Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.

Maintained by Guangchuang Yu. Last updated 8 months ago.

phylogenetic-tree tidyverse tree-data

5.8 match 54 stars 13.25 score 584 scripts 128 dependents

braverock

PerformanceAnalytics:Econometric Tools for Performance and Risk Analysis

Collection of econometric functions for performance and risk analysis. In addition to standard risk and performance metrics, this package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible.

Maintained by Brian G. Peterson. Last updated 3 months ago.

4.8 match 222 stars 15.93 score 4.8k scripts 20 dependents

tidyverts

tsibble:Tidy Temporal Data Frames and Tools

Provides a 'tbl_ts' class (the 'tsibble') for temporal data in an data- and model-oriented format. The 'tsibble' provides tools to easily manipulate and analyse temporal data, such as filling in time gaps and aggregating over calendar periods.

Maintained by Earo Wang. Last updated 2 months ago.

5.3 match 538 stars 14.47 score 4.4k scripts 42 dependents

ropensci

vcr:Record 'HTTP' Calls to Disk

Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.

Maintained by Scott Chamberlain. Last updated 12 days ago.

http https api web-services curl mock mocking http-mocking testing testing-tools tdd unit-testing vcr

7.5 match 77 stars 10.06 score 165 scripts

r-lib

httr:Tools for Working with URLs and HTTP

Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).

Maintained by Hadley Wickham. Last updated 1 years ago.

api curl http

3.6 match 989 stars 20.56 score 29k scripts 4.3k dependents

rcppcore

RcppParallel:Parallel Programming Tools for 'Rcpp'

High level functions for parallel programming with 'Rcpp'. For example, the 'parallelFor()' function can be used to convert the work of a standard serial "for" loop into a parallel one and the 'parallelReduce()' function can be used for accumulating aggregate or other values.

Maintained by Kevin Ushey. Last updated 2 months ago.

onetbb cpp

5.0 match 173 stars 14.89 score 215 scripts 790 dependents

florianhartig

BayesianTools:General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics

General-purpose MCMC and SMC samplers, as well as plots and diagnostic functions for Bayesian statistics, with a particular focus on calibrating complex system models. Implemented samplers include various Metropolis MCMC variants (including adaptive and/or delayed rejection MH), the T-walk, two differential evolution MCMCs, two DREAM MCMCs, and a sequential Monte Carlo (SMC) particle filter.

Maintained by Florian Hartig. Last updated 1 years ago.

bayes ecological-models mcmc optimization smc systems-biology cpp

7.3 match 122 stars 10.17 score 580 scripts 5 dependents

polkas

pacs:Supplementary Tools for R Packages Developers

Supplementary utils for CRAN maintainers and R packages developers. Validating the library, packages and lock files. Exploring a complexity of a specific package like evaluating its size in bytes with all dependencies. The shiny app complexity could be explored too. Assessing the life duration of a specific package version. Checking a CRAN package check page status for any errors and warnings. Retrieving a DESCRIPTION or NAMESPACE file for any package version. Comparing DESCRIPTION or NAMESPACE files between different package versions. Getting a list of all releases for a specific package. The Bioconductor is partly supported.

Maintained by Maciej Nasinski. Last updated 6 months ago.

bioconductor dependencies library lifeduration renv shiny tools utils

13.0 match 25 stars 5.70 score 8 scripts

ices-tools-prod

icesVocab:ICES Vocabularies Database Web Services

R interface to access the Vocabularies REST API of the ICES (International Council for the Exploration of the Sea) Vocabularies database <https://vocab.ices.dk/services/>.

Maintained by Colin Millar. Last updated 1 months ago.

13.3 match 6 stars 5.55 score 78 scripts 5 dependents

tidyverse

purrr:Functional Programming Tools

A complete and consistent functional programming toolkit for R.

Maintained by Hadley Wickham. Last updated 1 months ago.

functional-programming

3.3 match 1.3k stars 22.12 score 59k scripts 6.9k dependents

rvlenth

estimability:Tools for Assessing Estimability of Linear Predictions

Provides tools for determining estimability of linear functions of regression coefficients, and 'epredict' methods that handle non-estimable cases correctly. Estimability theory is discussed in many linear-models textbooks including Chapter 3 of Monahan, JF (2008), "A Primer on Linear Models", Chapman and Hall (ISBN 978-1-4200-6201-4).

Maintained by Russell Lenth. Last updated 9 months ago.

7.6 match 2 stars 9.64 score 18 scripts 242 dependents

bioc

psichomics:Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

Maintained by Nuno Saraiva-Agostinho. Last updated 5 months ago.

sequencing rnaseq alternativesplicing differentialsplicing transcription gui principalcomponent survival biomedicalinformatics transcriptomics immunooncology visualization multiplecomparison geneexpression differentialexpression alternative-splicing bioconductor data-analyses differential-gene-expression differential-splicing-analysis gene-expression gtex recount2 rna-seq-data splicing-quantification sra tcga vast-tools cpp

10.6 match 36 stars 6.95 score 31 scripts

ropensci

srr:'rOpenSci' Review Roclets

Companion package to 'rOpenSci' statistical software review project.

Maintained by Mark Padgham. Last updated 5 months ago.

compliance-automation statistical-software cpp

13.3 match 5 stars 5.52 score 3 scripts 2 dependents

simsem

semTools:Useful Tools for Structural Equation Modeling

Provides miscellaneous tools for structural equation modeling, many of which extend the 'lavaan' package. For example, latent interactions can be estimated using product indicators (Lin et al., 2010, <doi:10.1080/10705511.2010.488999>) and simple effects probed; analytical power analyses can be conducted (Jak et al., 2021, <doi:10.3758/s13428-020-01479-0>); and scale reliability can be estimated based on estimated factor-model parameters.

Maintained by Terrence D. Jorgensen. Last updated 3 days ago.

5.3 match 79 stars 13.74 score 1.1k scripts 31 dependents

jmazucheli

mle.tools:Expected/Observed Fisher Information and Bias-Corrected Maximum Likelihood Estimate(s)

Calculates the expected/observed Fisher information and the bias-corrected maximum likelihood estimate(s) via Cox-Snell Methodology.

Maintained by Josmar Mazucheli. Last updated 8 years ago.

37.5 match 1 stars 1.91 score 27 scripts 1 dependents

nashjc

nlsr:Functions for Nonlinear Least Squares Solutions - Updated 2022

Provides tools for working with nonlinear least squares problems. For the estimation of models reliable and robust tools than nls(), where the the Gauss-Newton method frequently stops with 'singular gradient' messages. This is accomplished by using, where possible, analytic derivatives to compute the matrix of derivatives and a stabilization of the solution of the estimation equations. Tools for approximate or externally supplied derivative matrices are included. Bounds and masks on parameters are handled properly.

Maintained by John C Nash. Last updated 27 days ago.

10.1 match 7.02 score 94 scripts 5 dependents

stevenpawley

Rsagacmd:Linking R with the Open-Source 'SAGA-GIS' Software

Provides an R scripting interface to the open-source 'SAGA-GIS' (System for Automated Geoscientific Analyses Geographical Information System) software. 'Rsagacmd' dynamically generates R functions for every 'SAGA-GIS' geoprocessing tool based on the user's currently installed 'SAGA-GIS' version. These functions are contained within an S3 object and are accessed as a named list of libraries and tools. This structure facilitates an easier scripting experience by organizing the large number of 'SAGA-GIS' geoprocessing tools (>700) by their respective library. Interactive scripting can fully take advantage of code autocompletion tools (e.g. in 'RStudio'), allowing for each tools syntax to be quickly recognized. Furthermore, the most common types of spatial data (via the 'terra', 'sp', and 'sf' packages) along with non-spatial data are automatically passed from R to the 'SAGA-GIS' command line tool for geoprocessing operations, and the results are loaded as the appropriate R object. Outputs from individual 'SAGA-GIS' tools can also be chained using pipes from the 'magrittr' and 'dplyr' packages to combine complex geoprocessing operations together in a single statement. 'SAGA-GIS' is available under a GPLv2 / LGPLv2 licence from <https://sourceforge.net/projects/saga-gis/> including Windows x86/x64 and macOS binaries. SAGA-GIS is also included in Debian/Ubuntu default software repositories. Rsagacmd has currently been tested on 'SAGA-GIS' versions from 2.3.1 to 9.5.1 on Windows, Linux and macOS.

Maintained by Steven Pawley. Last updated 6 months ago.

11.3 match 32 stars 6.27 score 77 scripts

r-gregmisc

gdata:Various R Programming Tools for Data Manipulation

Various R programming tools for data manipulation, including medical unit conversions, combining objects, character vector operations, factor manipulation, obtaining information about R objects, generating fixed-width format files, extracting components of date & time objects, operations on columns of data frames, matrix operations, operations on vectors, operations on data frames, value of last evaluated expression, and a resample() wrapper for sample() that ensures consistent behavior for both scalar and vector arguments.

Maintained by Arni Magnusson. Last updated 2 months ago.

5.2 match 9 stars 13.62 score 4.5k scripts 124 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 27 days ago.

13.3 match 4 stars 5.28 score

pasraia

RRphylo:Phylogenetic Ridge Regression Methods for Comparative Studies

Functions for phylogenetic analysis (Castiglione et al., 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.

Maintained by Silvia Castiglione. Last updated 7 months ago.

9.4 match 10 stars 7.48 score 83 scripts

mcguinlu

robvis:Visualize the Results of Risk-of-Bias (ROB) Assessments

Helps users in quickly visualizing risk-of-bias assessments performed as part of a systematic review. It allows users to create weighted bar-plots of the distribution of risk-of-bias judgments within each bias domain, in addition to traffic-light plots of the specific domain-level judgments for each study. The resulting figures are of publication quality and are formatted according the risk-of-bias assessment tool use to perform the assessments. Currently, the supported tools are ROB2.0 (for randomized controlled trials; Sterne et al (2019) <doi:10.1136/bmj.l4898>), ROBINS-I (for non-randomised studies of interventions; Sterne (2016) <doi:10.1136/bmj.i4919>), and Quality & Applicability of Diagnostic Accuracy Studies V2 (Whiting et al (2011) <doi:10.7326/0003-4819-155-8-201110180-00009>), and QUIPS (Hayden et al (2013) <doi:10.7326/0003-4819-158-4-201302190-00009>.

Maintained by Luke McGuinness. Last updated 2 years ago.

evidence-synthesis risk-of-bias systematic-reviews visualisation

8.8 match 59 stars 7.99 score 67 scripts

ropensci

pkgmatch:Find R Packages Matching Either Descriptions or Other R Packages

Find R packages matching either descriptions or other R packages.

Maintained by Mark Padgham. Last updated 1 months ago.

embeddings llms natural-language-processing cpp

13.3 match 3 stars 5.23 score

dcomtois

summarytools:Tools to Quickly and Neatly Summarize Data

Data frame summaries, cross-tabulations, weight-enabled frequency tables and common descriptive (univariate) statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.

Maintained by Dominic Comtois. Last updated 15 hours ago.

descriptive-statistics frequency-table html-report markdown pander pandoc pandoc-markdown rmarkdown rstudio

4.8 match 526 stars 14.52 score 2.9k scripts 6 dependents

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

3.5 match 2.4k stars 19.51 score 51k scripts 148 dependents

ices-tools-prod

icesAdvice:Functions Related to ICES Advice

A collection of functions that facilitate computational steps related to advice for fisheries management, according to ICES guidelines. These include methods for calculating reference points and model diagnostics.

Maintained by Colin Millar. Last updated 1 years ago.

13.3 match 7 stars 5.14 score 66 scripts 2 dependents

canmod

LBoM.tools:Tools for Curating London Bills of Mortality and Registrar General Data

Part of an open toolchain for processing infectious disease datasets available through the IIDDA data repository.

Maintained by Steve Walker. Last updated 6 months ago.

40.3 match 1.70 score

r-tmap

tmaptools:Thematic Map Tools

Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.

Maintained by Martijn Tennekes. Last updated 2 months ago.

5.9 match 42 stars 11.67 score 1.8k scripts 26 dependents

hadley

pryr:Tools for Computing on the Language

Useful tools to pry back the covers of R and understand the language at a deeper level.

Maintained by Hadley Wickham. Last updated 1 years ago.

cpp

5.8 match 204 stars 11.85 score 1.9k scripts 56 dependents

tidyverts

fabletools:Core Tools for Packages in the 'fable' Framework

Provides tools, helpers and data structures for developing models and time series functions for 'fable' and extension packages. These tools support a consistent and tidy interface for time series modelling and analysis.

Maintained by Mitchell OHara-Wild. Last updated 1 months ago.

5.6 match 91 stars 12.18 score 396 scripts 18 dependents

tidyverse

tidyverse:Easily Install and Load the 'Tidyverse'

The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step. Learn more about the 'tidyverse' at <https://www.tidyverse.org>.

Maintained by Hadley Wickham. Last updated 5 months ago.

data-science tidyverse

3.3 match 1.7k stars 20.26 score 664k scripts 125 dependents

ironholds

urltools:Vectorised Tools for URL Handling and Parsing

A toolkit for all URL-handling needs, including encoding and decoding, parsing, parameter extraction and modification. All functions are designed to be both fast and entirely vectorised. It is intended to be useful for people dealing with web-related datasets, such as server-side logs, although may be useful for other situations involving large sets of URLs.

Maintained by Os Keyes. Last updated 4 years ago.

access-logs data-import url cpp

5.0 match 131 stars 13.43 score 968 scripts 264 dependents

evalclass

prcbench:Testing Workbench for Precision-Recall Curves

A testing workbench to evaluate tools that calculate precision-recall curves. Saito and Rehmsmeier (2015) <doi:10.1371/journal.pone.0118432>.

Maintained by Takaya Saito. Last updated 2 years ago.

cpp

14.2 match 5 stars 4.72 score 21 scripts

wahani

dat:Tools for Data Manipulation

An implementation of common higher order functions with syntactic sugar for anonymous function. Provides also a link to 'dplyr' and 'data.table' for common transformations on data frames to work around non standard evaluation by default.

Maintained by Sebastian Warnholz. Last updated 4 years ago.

10.0 match 16 stars 6.66 score 32 scripts 1 dependents

bioc

MSstatsConvert:Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

MSstatsConvert provides tools for importing reports of Mass Spectrometry data processing tools into R format suitable for statistical analysis using the MSstats and MSstatsTMT packages.

Maintained by Mateusz Staniak. Last updated 3 months ago.

massspectrometry proteomics software dataimport qualitycontrol

10.4 match 6.37 score 25 scripts 7 dependents

ropensci

webmockr:Stubbing and Setting Expectations on 'HTTP' Requests

Stubbing and setting expectations on 'HTTP' requests. Includes tools for stubbing 'HTTP' requests, including expected request conditions and response conditions. Match on 'HTTP' method, query parameters, request body, headers and more. Can be used for unit tests or outside of a testing context.

Maintained by Scott Chamberlain. Last updated 1 months ago.

http https api web-services curl mock mocking fakeweb http-mocking testing testing-tools tdd http-mock

8.0 match 49 stars 8.29 score 141 scripts 1 dependents

tidyverse

forcats:Tools for Working with Categorical Variables (Factors)

Helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, 'anonymising', and manually 'recoding').

Maintained by Hadley Wickham. Last updated 1 years ago.

factor tidyverse

3.5 match 555 stars 18.77 score 21k scripts 1.2k dependents

liamrevell

phytools:Phylogenetic Tools for Comparative Biology (and Other Things)

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Maintained by Liam J. Revell. Last updated 27 days ago.

4.8 match 218 stars 13.85 score 4.8k scripts 76 dependents

simongrund1

mitml:Tools for Multiple Imputation in Multilevel Modeling

Provides tools for multiple imputation of missing data in multilevel modeling. Includes a user-friendly interface to the packages 'pan' and 'jomo', and several functions for visualization, data management and the analysis of multiply imputed data sets.

Maintained by Simon Grund. Last updated 1 years ago.

imputation missing-data mixed-effects multilevel-data multilevel-models

5.3 match 29 stars 12.36 score 246 scripts 153 dependents

vegandevs

vegan:Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Maintained by Jari Oksanen. Last updated 16 days ago.

ecological-modelling ecology ordination fortran openblas

3.3 match 472 stars 19.41 score 15k scripts 440 dependents

bioc

rBLAST:R Interface for the Basic Local Alignment Search Tool

Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) running locally to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.

Maintained by Michael Hahsler. Last updated 2 months ago.

genetics sequencing sequencematching alignment dataimport bioconductor bioinformatics blast-search

7.9 match 106 stars 8.07 score 106 scripts

hadley

plyr:Tools for Splitting, Applying and Combining Data

A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. The development of 'plyr' has been generously supported by 'Becton Dickinson'.

Maintained by Hadley Wickham. Last updated 4 months ago.

cpp

3.5 match 500 stars 18.16 score 83k scripts 3.3k dependents

uofuepibio

epiworldR:Fast Agent-Based Epi Models

A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.

Maintained by Andrew Pulsipher. Last updated 11 days ago.

abm agent-based-modeling covid-19 epidemics epidemiology r-programming rpack rpkg seir seir-model simulation sir sir-model cpp openmp

7.6 match 9 stars 8.33 score 58 scripts 1 dependents

trinker

textclean:Text Cleaning Tools

Tools to clean and process text. Tools are geared at checking for substrings that are not optimal for analysis and replacing or removing them (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen, Kumar, Ostendorf, & Richards (2001) <doi:10.1006/csla.2001.0169>) or extracting them into new variables. For example, emoticons are often used in text but not always easily handled by analysis algorithms. The replace_emoticon() function replaces emoticons with word equivalents.

Maintained by Tyler Rinker. Last updated 3 years ago.

data-munging emoticons regex text-analysis text-cleaning

6.1 match 248 stars 10.08 score 760 scripts 22 dependents

bioc

singleCellTK:Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.

Maintained by Joshua David Campbell. Last updated 23 days ago.

singlecell geneexpression differentialexpression alignment clustering immunooncology batcheffect normalization qualitycontrol dataimport gui

6.1 match 181 stars 10.16 score 252 scripts

r-lib

debugme:Debug R Packages

Specify debug messages as special string constants, and control debugging of packages via environment variables.

Maintained by Gábor Csárdi. Last updated 7 months ago.

debugging-tool

7.5 match 152 stars 8.20 score 11 scripts 7 dependents

juliasilge

tidytext:Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools

Using tidy data principles can make many text mining tasks easier, more effective, and consistent with tools already in wide use. Much of the infrastructure needed for text mining with tidy data frames already exists in packages like 'dplyr', 'broom', 'tidyr', and 'ggplot2'. In this package, we provide functions and supporting data sets to allow conversion of text to and from tidy formats, and to switch seamlessly between tidy tools and existing text mining packages.

Maintained by Julia Silge. Last updated 11 months ago.

natural-language-processing text-mining tidy-data tidyverse

3.6 match 1.2k stars 16.86 score 17k scripts 61 dependents

ropengov

eurostat:Tools for Eurostat Open Data

Tools to download data from the Eurostat database <https://ec.europa.eu/eurostat> together with search and manipulation utilities.

Maintained by Leo Lahti. Last updated 27 days ago.

ropengov eurostat eurostat-data

5.5 match 239 stars 11.09 score 892 scripts 5 dependents

sciviews

svUnit:'SciViews' - Unit, Integration and System Testing

A complete unit test system.

Maintained by Philippe Grosjean. Last updated 3 years ago.

sciviews testing-tools

7.5 match 3 stars 8.07 score 72 scripts 28 dependents

rinterface

shinyMobile:Mobile Ready 'shiny' Apps with Standalone Capabilities

Develop outstanding 'shiny' apps for 'iOS' and 'Android' as well as beautiful 'shiny' gadgets. 'shinyMobile' is built on top of the latest 'Framework7' template <https://framework7.io>. Discover 14 new input widgets (sliders, vertical sliders, stepper, grouped action buttons, toggles, picker, smart select, ...), 2 themes (light and dark), 12 new widgets (expandable cards, badges, chips, timelines, gauges, progress bars, ...) combined with the power of server-side notifications such as alerts, modals, toasts, action sheets, sheets (and more) as well as 3 layouts (single, tabs and split).

Maintained by David Granjon. Last updated 2 months ago.

android hacktoberfest2022 pwa shiny shinyapps template

5.1 match 409 stars 11.91 score 1.1k scripts 2 dependents

ropensci

repometrics:Metrics for Your Code Repository

Metrics for your code repository. Call one function to generate an interactive dashboard displaying the state of your code.

Maintained by Mark Padgham. Last updated 4 days ago.

dashboard software-metrics

13.3 match 2 stars 4.53 score

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

8.6 match 29 stars 6.96 score 45 scripts

bioc

TSCAN:Tools for Single-Cell Analysis

Provides methods to perform trajectory analysis based on a minimum spanning tree constructed from cluster centroids. Computes pseudotemporal cell orderings by mapping cells in each cluster (or new cells) to the closest edge in the tree. Uses linear modelling to identify differentially expressed genes along each path through the tree. Several plotting and interactive visualization functions are also implemented.

Maintained by Zhicheng Ji. Last updated 5 months ago.

geneexpression visualization gui

7.9 match 7.58 score 207 scripts 3 dependents

ms609

Quartet:Comparison of Phylogenetic Trees Using Quartet and Split Measures

Calculates the number of four-taxon subtrees consistent with a pair of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986), Reconstructing the shape of a tree from observed dissimilarity data, Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>, and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for computing the quartet and triplet distances between binary or general trees, Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157> for pairs of binary trees.

Maintained by Martin R. Smith. Last updated 2 months ago.

bioinformatics comparison phylogenetic-trees phylogenetics quartet quartet-distance research-tool tree cpp

7.5 match 14 stars 8.00 score 40 scripts

kwstat

pals:Color Palettes, Colormaps, and Tools to Evaluate Them

A comprehensive collection of color palettes, colormaps, and tools to evaluate them. See Kovesi (2015) <doi:10.48550/arXiv.1509.03700>.

Maintained by Kevin Wright. Last updated 9 days ago.

5.2 match 83 stars 11.39 score 2.1k scripts 8 dependents

ms609

TreeSearch:Phylogenetic Analysis with Discrete Character Data

Reconstruct phylogenetic trees from discrete data. Inapplicable character states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy" library, under equal or implied step weights. Contains a "shiny" user interface for interactive tree search and exploration of results, including character visualization, rogue taxon detection, tree space mapping, and cluster consensus trees (Smith 2022a, b) <doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>. Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, Successive Approximations (Farris, 1969) <doi:10.2307/2412182> and custom optimality criteria are implemented.

Maintained by Martin R. Smith. Last updated 3 days ago.

bioinformatics morphological-analysis phylogenetics research-tool tree-search cpp

7.5 match 7 stars 7.89 score 51 scripts

thinkr-open

golem:A Framework for Robust Shiny Applications

An opinionated framework for building a production-ready 'Shiny' application. This package contains a series of tools for building a robust 'Shiny' application from start to finish.

Maintained by Colin Fay. Last updated 7 months ago.

golemverse hacktoberfest shiny shiny-apps shiny-r shinyapps

4.1 match 921 stars 14.23 score 167 scripts 62 dependents

dasonk

docstring:Provides Docstring Capabilities to R Functions

Provides the ability to display something analogous to Python's docstrings within R. By allowing the user to document their functions as comments at the beginning of their function without requiring putting the function into a package we allow more users to easily provide documentation for their functions. The documentation can be viewed just like any other help files for functions provided by packages as well.

Maintained by Dason Kurkiewicz. Last updated 3 years ago.

devtools docstring documentation documentation-tool roxygen-style

7.5 match 57 stars 7.77 score 305 scripts 1 dependents

choonghyunryu

dlookr:Tools for Data Diagnosis, Exploration, Transformation

A collection of tools that support data diagnosis, exploration, and transformation. Data diagnostics provides information and visualization of missing values, outliers, and unique and negative values to help you understand the distribution and quality of your data. Data exploration provides information and visualization of the descriptive statistics of univariate variables, normality tests and outliers, correlation of two variables, and the relationship between the target variable and predictor. Data transformation supports binning for categorizing continuous variables, imputes missing values and outliers, and resolves skewness. And it creates automated reports that support these three tasks.

Maintained by Choonghyun Ryu. Last updated 9 months ago.

5.3 match 212 stars 11.05 score 748 scripts 2 dependents

aloy

HLMdiag:Diagnostic Tools for Hierarchical (Multilevel) Linear Models

A suite of diagnostic tools for hierarchical (multilevel) linear models. The tools include not only leverage and traditional deletion diagnostics (Cook's distance, covratio, covtrace, and MDFFITS) but also convenience functions and graphics for residual analysis. Models can be fit using either lmer in the 'lme4' package or lme in the 'nlme' package.

Maintained by Adam Loy. Last updated 4 years ago.

openblas cpp

6.6 match 17 stars 8.63 score 170 scripts 7 dependents

pik-piam

magclass:Data Class and Tools for Handling Spatial-Temporal Data

Data class for increased interoperability working with spatial-temporal data together with corresponding functions and methods (conversions, basic calculations and basic data manipulation). The class distinguishes between spatial, temporal and other dimensions to facilitate the development and interoperability of tools build for it. Additional features are name-based addressing of data and internal consistency checks (e.g. checking for the right data order in calculations).

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

5.1 match 5 stars 11.16 score 412 scripts 56 dependents

siacus

cem:Coarsened Exact Matching

Implementation of the Coarsened Exact Matching algorithm discussed along with its properties in Iacus, King, Porro (2011) <DOI:10.1198/jasa.2011.tm09599>; Iacus, King, Porro (2012) <DOI:10.1093/pan/mpr013> and Iacus, King, Porro (2019) <DOI:10.1017/pan.2018.29>.

Maintained by Stefano M. Iacus. Last updated 3 years ago.

9.8 match 2 stars 5.76 score 239 scripts 1 dependents

business-science

modeltime:The Tidymodels Extension for Time Series Modeling

The time series forecasting framework for use with the 'tidymodels' ecosystem. Models include ARIMA, Exponential Smoothing, and additional time series models from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition" (<https://otexts.com/fpp2/>). Refer to "Prophet: forecasting at scale" (<https://research.facebook.com/blog/2017/02/prophet-forecasting-at-scale/>.).

Maintained by Matt Dancho. Last updated 5 months ago.

arima data-science deep-learning ets forecasting machine-learning machine-learning-algorithms modeltime prophet tbats tidymodeling tidymodels time time-series time-series-analysis timeseries timeseries-forecasting

5.3 match 549 stars 10.57 score 1.1k scripts 7 dependents

mllg

batchtools:Tools for Computation on Batch Systems

As a successor of the packages 'BatchJobs' and 'BatchExperiments', this package provides a parallel implementation of the Map function for high performance computing systems managed by schedulers 'IBM Spectrum LSF' (<https://www.ibm.com/products/hpc-workload-management>), 'OpenLava' (<https://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid Engine' (<https://www.univa.com/>), 'Slurm' (<https://slurm.schedmd.com/>), 'TORQUE/PBS' (<https://adaptivecomputing.com/cherry-services/torque-resource-manager/>), or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>). A multicore and socket mode allow the parallelization on a local machines, and multiple machines can be hooked up via SSH to create a makeshift cluster. Moreover, the package provides an abstraction mechanism to define large-scale computer experiments in a well-organized and reproducible way.

Maintained by Michel Lang. Last updated 2 years ago.

batchexperiments batchjobs docker-swarm high-performance-computing hpc hpc-clusters lsf openlava parallel-computing reproducibility sge slurm torque

4.9 match 175 stars 11.39 score 772 scripts 14 dependents

r-lib

evaluate:Parsing and Evaluation Tools that Provide More Details than the Default

Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.

Maintained by Hadley Wickham. Last updated 2 months ago.

evaluation parsing repl

3.5 match 135 stars 16.14 score 183 scripts 4.5k dependents

sfirke

janitor:Simple Tools for Examining and Cleaning Dirty Data

The main janitor functions can: perfectly format data.frame column names; provide quick counts of variable combinations (i.e., frequency tables and crosstabs); and explore duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and-report functions approximate popular features of SPSS and Microsoft Excel. This package follows the principles of the "tidyverse" and works well with the pipe function %>%. janitor was built with beginning-to-intermediate R users in mind and is optimized for user-friendliness.

Maintained by Sam Firke. Last updated 3 months ago.

data-analysis data-cleaning data-science dirty-data excel pivot-tables spss tabulations tidyverse

2.9 match 1.4k stars 19.15 score 35k scripts 231 dependents

mlcollyer

RRPP:Linear Model Evaluation with Randomized Residuals in a Permutation Procedure

Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are calculated over many permutations to generate empirical probability distributions for evaluating model effects. Additionally, coefficients, statistics, fitted values, and residuals generated over many permutations can be used for various procedures including pairwise tests, prediction, classification, and model comparison. This package should provide most tools one could need for the analysis of high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.

Maintained by Michael Collyer. Last updated 26 days ago.

5.7 match 4 stars 9.84 score 173 scripts 7 dependents

fellstat

ipc:Tools for Message Passing Between Processes

Provides tools for passing messages between R processes. Shiny examples are provided showing how to perform useful tasks such as: updating reactive values from within a future, progress bars for long running async tasks, and interrupting async tasks based on user input.

Maintained by Ian E. Fellows. Last updated 2 years ago.

8.5 match 56 stars 6.50 score 38 scripts 1 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

3.9 match 315 stars 14.24 score 14k scripts 10 dependents

jsugarelli

debugr:Debug Tool to Watch Objects/Expressions While Running an R Script

Tool to print out the value of R objects/expressions while running an R script. Outputs can be made dependent on user-defined conditions/criteria. Debug messages only appear when a global option for debugging is set. This way, 'debugr' code can even remain in the debugged code for later use without any negative effects during normal runtime.

Maintained by Joachim Zuckarelli. Last updated 7 years ago.

debugger debugging debugging-tool

10.8 match 17 stars 5.04 score 13 scripts

wch

extrafont:Tools for Using Fonts

Tools to using fonts other than the standard PostScript fonts. This package makes it easy to use system TrueType fonts and with PDF or PostScript output files, and with bitmap output files in Windows. extrafont can also be used with fonts packaged specifically to be used with, such as the fontcm package, which has Computer Modern PostScript fonts with math symbols.

Maintained by Winston Chang. Last updated 2 years ago.

3.8 match 324 stars 14.10 score 13k scripts 51 dependents

trinker

textshape:Tools for Reshaping Text

Tools that can be used to reshape and restructure text data.

Maintained by Tyler Rinker. Last updated 12 months ago.

data-reshaping manipulation sentence-boundary-detection text-data text-formating tidy

5.9 match 50 stars 9.18 score 266 scripts 34 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 4 months ago.

clinical-trials ectd packaging-tool pharmaverse

8.0 match 29 stars 6.75 score 12 scripts

easystats

datawizard:Easy Data Wrangling and Statistical Transformations

A lightweight package to assist in key steps involved in any data analysis workflow: (1) wrangling the raw data to get it in the needed form, (2) applying preprocessing steps and statistical transformations, and (3) compute statistical summaries of data properties and distributions. It is also the data wrangling backend for packages in 'easystats' ecosystem. References: Patil et al. (2022) <doi:10.21105/joss.04684>.

Maintained by Etienne Bacher. Last updated 9 days ago.

data dplyr hacktoberfest janitor manipulation reshape tidyr wrangling

3.6 match 222 stars 14.71 score 436 scripts 119 dependents

yihui

knitr:A General-Purpose Package for Dynamic Report Generation in R

Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

Maintained by Yihui Xie. Last updated 1 days ago.

dynamic-documents knitr literate-programming rmarkdown sweave

2.3 match 2.4k stars 23.62 score 116k scripts 4.2k dependents

ropensci

babeldown:Helpers for Automatic Translation of Markdown-based Content

Provide workflows and guidance for automatic translation of Markdown-based R content using DeepL API.

Maintained by Maëlle Salmon. Last updated 24 days ago.

13.3 match 22 stars 4.00 score 3 scripts

ltierney

codetools:Code Analysis Tools for R

Code analysis tools for R.

Maintained by Luke Tierney. Last updated 12 months ago.

5.5 match 9.64 score 274 scripts 4.5k dependents

bioc

txdbmaker:Tools for making TxDb objects from genomic annotations

A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

Maintained by H. Pagès. Last updated 4 months ago.

infrastructure dataimport annotation genomeannotation genomeassembly genetics sequencing bioconductor-package core-package

5.5 match 3 stars 9.70 score 92 scripts 86 dependents

edzer

intervals:Tools for Working with Points and Intervals

Tools for working with and comparing sets of points and intervals.

Maintained by Edzer Pebesma. Last updated 7 months ago.

cpp

5.6 match 11 stars 9.40 score 122 scripts 90 dependents

bioc

IsoformSwitchAnalyzeR:Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

Maintained by Kristoffer Vitting-Seerup. Last updated 5 months ago.

geneexpression transcription alternativesplicing differentialexpression differentialsplicing visualization statisticalmethod transcriptomevariant biomedicalinformatics functionalgenomics systemsbiology transcriptomics rnaseq annotation functionalprediction geneprediction dataimport multiplecomparison batcheffect immunooncology

5.6 match 108 stars 9.26 score 125 scripts

ices-tools-prod

msy:Estimation of Equilibrium Reference Points for Fsisheries

Methods to estimate equilibrium reference points for fisheries data. Currently data must be converted into FLStock objects of the FLR (Fisheries Library in R) style, defined in the R package FLCore.

Maintained by Colin Millar. Last updated 2 years ago.

13.3 match 13 stars 3.91 score 42 scripts

lcrawlab

mvMAPIT:Multivariate Genome Wide Marginal Epistasis Test

Epistasis, commonly defined as the interaction between genetic loci, is known to play an important role in the phenotypic variation of complex traits. As a result, many statistical methods have been developed to identify genetic variants that are involved in epistasis, and nearly all of these approaches carry out this task by focusing on analyzing one trait at a time. Previous studies have shown that jointly modeling multiple phenotypes can often dramatically increase statistical power for association mapping. In this package, we present the 'multivariate MArginal ePIstasis Test' ('mvMAPIT') – a multi-outcome generalization of a recently proposed epistatic detection method which seeks to detect marginal epistasis or the combined pairwise interaction effects between a given variant and all other variants. By searching for marginal epistatic effects, one can identify genetic variants that are involved in epistasis without the need to identify the exact partners with which the variants interact – thus, potentially alleviating much of the statistical and computational burden associated with conventional explicit search based methods. Our proposed 'mvMAPIT' builds upon this strategy by taking advantage of correlation structure between traits to improve the identification of variants involved in epistasis. We formulate 'mvMAPIT' as a multivariate linear mixed model and develop a multi-trait variance component estimation algorithm for efficient parameter inference and P-value computation. Together with reasonable model approximations, our proposed approach is scalable to moderately sized genome-wide association studies. Crawford et al. (2017) <doi:10.1371/journal.pgen.1006869>. Stamp et al. (2023) <doi:10.1093/g3journal/jkad118>.

Maintained by Julian Stamp. Last updated 5 months ago.

cpp epistasis epistasis-analysis gwas gwas-tools linear-mixed-models mapit mvmapit variance-components openblas cpp openmp

7.5 match 11 stars 6.90 score 17 scripts 1 dependents

talgalili

gplots:Various R Programming Tools for Plotting Data

Various R programming tools for plotting data, including: - calculating and plotting locally smoothed summary function as ('bandplot', 'wapply'), - enhanced versions of standard plots ('barplot2', 'boxplot2', 'heatmap.2', 'smartlegend'), - manipulating colors ('col2hex', 'colorpanel', 'redgreen', 'greenred', 'bluered', 'redblue', 'rich.colors'), - calculating and plotting two-dimensional data summaries ('ci2d', 'hist2d'), - enhanced regression diagnostic plots ('lmplot2', 'residplot'), - formula-enabled interface to 'stats::lowess' function ('lowess'), - displaying textual data in plots ('textplot', 'sinkplot'), - plotting dots whose size reflects the relative magnitude of the elements ('balloonplot', 'bubbleplot'), - plotting "Venn" diagrams ('venn'), - displaying Open-Office style plots ('ooplot'), - plotting multiple data on same region, with separate axes ('overplot'), - plotting means and confidence intervals ('plotCI', 'plotmeans'), - spacing points in an x-y plot so they don't overlap ('space').

Maintained by Tal Galili. Last updated 5 months ago.

3.4 match 13 stars 15.11 score 13k scripts 482 dependents

tidymodels

recipes:Preprocessing and Feature Engineering Steps for Modeling

A recipe prepares your data for modeling. We provide an extensible framework for pipeable sequences of feature engineering steps provides preprocessing tools to be applied to data. Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting processed output can then be used as inputs for statistical or machine learning models.

Maintained by Max Kuhn. Last updated 5 days ago.

2.8 match 584 stars 18.71 score 7.2k scripts 380 dependents

bioc

SeqVarTools:Tools for variant data

An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.

Maintained by Stephanie M. Gogarten. Last updated 5 months ago.

snp geneticvariability sequencing genetics

5.9 match 3 stars 8.76 score 384 scripts 2 dependents

olangsrud

RegSDC:Information Preserving Regression-Based Tools for Statistical Disclosure Control

Implementation of the methods described in the paper with the above title: Langsrud, Ø. (2019) <doi:10.1007/s11222-018-9848-9>. The package can be used to generate synthetic or hybrid continuous microdata, and the relationship to the original data can be controlled in several ways. A function for replacing suppressed tabular cell frequencies with decimal numbers is included.

Maintained by Øyvind Langsrud. Last updated 3 days ago.

13.0 match 3.95 score 20 scripts 1 dependents

azure

AzureContainers:Interface to 'Container Instances', 'Docker Registry' and 'Kubernetes' in 'Azure'

An interface to container functionality in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/product-categories/containers/>. Manage 'Azure Container Instance' (ACI), 'Azure Container Registry' (ACR) and 'Azure Kubernetes Service' (AKS) resources, push and pull images, and deploy services. On the client side, lightweight shells to the 'docker', 'docker-compose', 'kubectl' and 'helm' commandline tools are provided. Part of the 'AzureR' family of packages.

Maintained by Hong Ooi. Last updated 2 years ago.

azure-container-instances azure-container-registry azure-kubernetes-service azure-sdk-r containers kubernetes

7.9 match 25 stars 6.49 score 57 scripts

jacob-long

jtools:Analysis and Presentation of Social Scientific Data

This is a collection of tools for more efficiently understanding and sharing the results of (primarily) regression analyses. There are also a number of miscellaneous functions for statistical and programming purposes. Support for models produced by the survey and lme4 packages are points of emphasis.

Maintained by Jacob A. Long. Last updated 6 months ago.

social-sciences

3.5 match 167 stars 14.48 score 4.0k scripts 14 dependents

trinker

qdapRegex:Regular Expression Removal, Extraction, and Replacement Tools

A collection of regular expression tools associated with the 'qdap' package that may be useful outside of the context of discourse analysis. Tools include removal/extraction/replacement of abbreviations, dates, dollar amounts, email addresses, hash tags, numbers, percentages, citations, person tags, phone numbers, times, and zip codes.

Maintained by Tyler Rinker. Last updated 1 years ago.

qdapregex regular-expression

5.4 match 50 stars 9.48 score 502 scripts 41 dependents

bioc

GWASTools:Tools for Genome Wide Association Studies

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

Maintained by Stephanie M. Gogarten. Last updated 5 months ago.

snp geneticvariability qualitycontrol microarray

4.8 match 17 stars 10.50 score 396 scripts 5 dependents

ices-tools-prod

icesDatsu:Functions to Interact with the ICES Data Submission Utility (DATSU)

Functions to Interact with the ICES Data Submission Utility (DATSU) <https://datsu.ices.dk/web/index.aspx>.

Maintained by Colin Millar. Last updated 5 months ago.

13.3 match 2 stars 3.78 score 2 scripts 2 dependents

r-lib

ellipsis:Tools for Working with ...

The ellipsis is a powerful tool for extending functions. Unfortunately this power comes at a cost: misspelled arguments will be silently ignored. The ellipsis package provides a collection of functions to catch problems and alert the user.

Maintained by Hadley Wickham. Last updated 4 years ago.

dot-dot-dot ellipsis

4.3 match 141 stars 11.72 score 83 scripts 249 dependents

sinhrks

ggfortify:Data Visualization Tools for Statistical Analysis Results

Unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis results and plots in a unified style using 'ggplot2'.

Maintained by Yuan Tang. Last updated 9 months ago.

3.4 match 529 stars 14.49 score 9.1k scripts 22 dependents

bioc

clusterProfiler:A universal enrichment tool for interpreting omics data

This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions.

Maintained by Guangchuang Yu. Last updated 4 months ago.

annotation clustering genesetenrichment go kegg multiplecomparison pathways reactome visualization enrichment-analysis gsea

2.9 match 1.1k stars 17.03 score 11k scripts 48 dependents

coffeemuggler

caTools:Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc

Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.

Maintained by Michael Dietze. Last updated 6 months ago.

cpp

4.4 match 8 stars 11.17 score 9.1k scripts 566 dependents

cwolock

survML:Tools for Flexible Survival Analysis Using Machine Learning

Statistical tools for analyzing time-to-event data using machine learning. Implements survival stacking for conditional survival estimation, standardized survival function estimation for current status data, and methods for algorithm-agnostic variable importance. See Wolock CJ, Gilbert PB, Simon N, and Carone M (2024) <doi:10.1080/10618600.2024.2304070>.

Maintained by Charles Wolock. Last updated 2 months ago.

6.1 match 16 stars 8.06 score 73 scripts 1 dependents

r-lidar

lasR:Fast and Pipeable Airborne LiDAR Data Tools

Fast and pipeable airborne lidar processing tools. Read/write 'las' and 'laz' files, computation of metrics in area based approach, point filtering, normalization, individual tree segmentation and other manipulations in a powerful and versatile processing chain.

Maintained by Jean-Romain Roussel. Last updated 21 days ago.

gdal cpp openmp

7.3 match 17 stars 6.76 score 26 scripts

ignacio82

vizdraws:Visualize Draws from the Prior and Posterior Distributions

Interactive visualization for Bayesian prior and posterior distributions. This package facilitates an animated transition between prior and posterior distributions. Additionally, it splits the distribution into bars based on the provided 'breaks,' displaying the probability for each region. If no 'breaks' are provided, it defaults to zero.

Maintained by Ignacio Martinez. Last updated 1 years ago.

bayesian visualization visualization-library visualization-tools

7.5 match 10 stars 6.56 score 7 scripts 2 dependents

s-u

base64enc:Tools for base64 Encoding

Tools for handling base64 encoding. It is more flexible than the orphaned base64 package.

Maintained by Simon Urbanek. Last updated 3 years ago.

3.9 match 9 stars 12.62 score 680 scripts 4.8k dependents

jeroen

js:Tools for Working with JavaScript in R

A set of utilities for working with JavaScript syntax in R. Includes tools to parse, tokenize, compile, validate, reformat, optimize and analyze JavaScript code.

Maintained by Jeroen Ooms. Last updated 5 months ago.

5.5 match 68 stars 8.87 score 83 scripts 1 dependents

ropensci

rix:Reproducible Data Science Environments with 'Nix'

Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.

Maintained by Bruno Rodrigues. Last updated 4 days ago.

nix peer-reviewed reproducibility reproducible-research

4.7 match 235 stars 10.54 score 67 scripts

doi-usgs

nhdplusTools:NHDPlus Tools

Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.

Maintained by David Blodgett. Last updated 25 days ago.

4.3 match 87 stars 11.38 score 348 scripts 5 dependents

ropensci

hddtools:Hydrological Data Discovery Tools

Tools to discover hydrological data, accessing catalogues and databases from various data providers. The package is described in Vitolo (2017) "hddtools: Hydrological Data Discovery Tools" <doi:10.21105/joss.00056>.

Maintained by Dorothea Hug Peter. Last updated 7 months ago.

data60uk grdc hydrology kgclimateclass mopex peer-reviewed precipitation sepa

8.7 match 48 stars 5.56 score 25 scripts

klmr

box:Write Reusable, Composable and Modular R Code

A modern module system for R. Organise code into hierarchical, composable, reusable modules, and use it effortlessly across projects via a flexible, declarative dependency loading syntax.

Maintained by Konrad Rudolph. Last updated 12 days ago.

modules packages

3.9 match 888 stars 12.39 score 47 scripts 4 dependents

gleon

rLakeAnalyzer:Lake Physics Tools

Standardized methods for calculating common important derived physical features of lakes including water density based based on temperature, thermal layers, thermocline depth, lake number, Wedderburn number, Schmidt stability and others.

Maintained by Luke Winslow. Last updated 4 years ago.

5.3 match 45 stars 9.05 score 280 scripts 1 dependents

trinker

textstem:Tools for Stemming and Lemmatizing Text

Tools that stem and lemmatize text. Stemming is a process that removes endings such as affixes. Lemmatization is the process of grouping inflected forms together as a single base form.

Maintained by Tyler Rinker. Last updated 7 years ago.

lemmatization stemming text-mining

5.5 match 45 stars 8.71 score 888 scripts 11 dependents

nhs-r-community

NHSRplotthedots:Draw XmR Charts for NHSE/I 'Making Data Count' Programme

Provides tools for drawing Statistical Process Control (SPC) charts. This package supports the NHSE/I programme 'Making Data Count', and allows users to draw XmR charts, use change points and apply rules with summary indicators for when rules are breached.

Maintained by Christopher Reading. Last updated 1 months ago.

ggplot2 nhs plotthedots spc xmr

5.8 match 49 stars 8.35 score 58 scripts

sciurus365

simlandr:Simulation-Based Landscape Construction for Dynamical Systems

A toolbox for constructing potential landscapes for dynamical systems using Monte Carlo simulation. The method is based on the potential landscape definition by Wang et al. (2008) <doi:10.1073/pnas.0800579105> (also see Zhou & Li, 2016 <doi:10.1063/1.4943096> for further mathematical discussions) and can be used for a large variety of models.

Maintained by Jingmeng Cui. Last updated 1 months ago.

research-tool

7.5 match 6 stars 6.41 score 12 scripts 2 dependents

ropenspain

climaemet:Climate AEMET Tools

Tools to download the climatic data of the Spanish Meteorological Agency (AEMET) directly from R using their API and create scientific graphs (climate charts, trend analysis of climate time series, temperature and precipitation anomalies maps, warming stripes graphics, climatograms, etc.).

Maintained by Diego Hernangómez. Last updated 1 months ago.

aemet climate data forecast-api ropenspain science spain weather-api

5.7 match 43 stars 8.32 score 59 scripts

rpahl

pipeflow:Lightweight, General-Purpose Data Analysis Pipelines

A lightweight yet powerful framework for building robust data analysis pipelines. With 'pipeflow', you initialize a pipeline with your dataset and construct workflows step by step by adding R functions. You can modify, remove, or insert steps and parameters at any stage, while 'pipeflow' ensures the pipeline's integrity. Overall, this package offers a beginner-friendly framework that simplifies and streamlines the development of data analysis pipelines by making them modular, intuitive, and adaptable.

Maintained by Roman Pahl. Last updated 2 months ago.

pipeline-tools reproducible-research

7.5 match 13 stars 6.35 score 19 scripts

tidymodels

tune:Tidy Tuning Tools

The ability to tune models is important. 'tune' contains functions and classes to be used in conjunction with other 'tidymodels' packages for finding reasonable values of hyper-parameters in models, pre-processing methods, and post-processing steps.

Maintained by Max Kuhn. Last updated 12 days ago.

3.3 match 293 stars 14.27 score 756 scripts 39 dependents

bioc

Rqc:Quality Control Tool for High-Throughput Sequencing Data

Rqc is an optimised tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.

Maintained by Welliton Souza. Last updated 5 months ago.

sequencing qualitycontrol dataimport cpp

7.9 match 6.00 score 67 scripts

inlabru-org

inlabru:Bayesian Latent Gaussian Modelling using INLA and Extensions

Facilitates spatial and general latent Gaussian modeling using integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) <doi:10.1111/2041-210X.13168>.

Maintained by Finn Lindgren. Last updated 3 days ago.

3.8 match 96 stars 12.62 score 832 scripts 6 dependents

martin3141

spant:MR Spectroscopy Analysis Tools

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.

Maintained by Martin Wilson. Last updated 30 days ago.

brain mri mrs mrshub spectroscopy fortran

5.5 match 24 stars 8.55 score 81 scripts

jwood000

RcppAlgos:High Performance Tools for Combinatorics and Computational Mathematics

Provides optimized functions and flexible iterators implemented in C++ for solving problems in combinatorics and computational mathematics. Handles various combinatorial objects including combinations, permutations, integer partitions and compositions, Cartesian products, unordered Cartesian products, and partition of groups. Utilizes the RMatrix class from 'RcppParallel' for thread safety. The combination and permutation functions contain constraint parameters that allow for generation of all results of a vector meeting specific criteria (e.g. finding all combinations such that the sum is between two bounds). Capable of ranking/unranking combinatorial objects efficiently (e.g. retrieve only the nth lexicographical result) which sets up nicely for parallelization as well as random sampling. Gmp support permits exploration where the total number of results is large (e.g. comboSample(10000, 500, n = 4)). Additionally, there are several high performance number theoretic functions that are useful for problems common in computational mathematics. Some of these functions make use of the fast integer division library 'libdivide'. The primeSieve function is based on the segmented sieve of Eratosthenes implementation by Kim Walisch. It is also efficient for large numbers by using the cache friendly improvements originally developed by Tomás Oliveira. Finally, there is a prime counting function that implements Legendre's formula based on the work of Kim Walisch.

Maintained by Joseph Wood. Last updated 1 months ago.

combinations combinatorics factorization number-theory parallel permutation prime-factorizations primesieve gmp cpp

4.7 match 45 stars 10.04 score 153 scripts 12 dependents

pacificcommunity

condor:Interact with 'Condor' from R via SSH

Interact with 'Condor' from R via SSH connection. Files are first uploaded from user machine to submitter machine, and the job is then submitted from the submitter machine to 'Condor'. Functions are provided to submit, list, and download 'Condor' jobs from R. 'Condor' is an open source high-throughput computing software framework for distributed parallelization of computationally intensive tasks.

Maintained by Arni Magnusson. Last updated 4 months ago.

htcondor ofp sam tool

11.0 match 5 stars 4.26 score 24 scripts

bioc

systemPipeR:systemPipeR: Workflow Environment for Data Analysis and Report Generation

systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.

Maintained by Thomas Girke. Last updated 5 months ago.

genetics infrastructure dataimport sequencing rnaseq riboseq chipseq methylseq snp geneexpression coverage genesetenrichment alignment qualitycontrol immunooncology reportwriting workflowstep workflowmanagement

4.0 match 53 stars 11.56 score 344 scripts 3 dependents

ices-tools-prod

icesDatsuQC:Run Quality Checks on Data Prior to Submission to ICES

Run quality checks on data sets using the same checks that are conducted on the ICES Data Submission Utility (DATSU) <https://datsu.ices.dk>.

Maintained by Colin Millar. Last updated 5 months ago.

13.3 match 2 stars 3.48 score 1 dependents

tidymodels

probably:Tools for Post-Processing Predicted Values

Models can be improved by post-processing class probabilities, by: recalibration, conversion to hard probabilities, assessment of equivocal zones, and other activities. 'probably' contains tools for conducting these operations as well as calibration tools and conformal inference techniques for regression models.

Maintained by Max Kuhn. Last updated 5 months ago.

3.8 match 115 stars 12.09 score 21k scripts 1 dependents

s-u

uuid:Tools for Generating and Handling of UUIDs

Tools for generating and handling of UUIDs (Universally Unique Identifiers).

Maintained by Simon Urbanek. Last updated 8 months ago.

3.7 match 26 stars 12.44 score 1.1k scripts 701 dependents

hughjonesd

santoku:A Versatile Cutting Tool

A tool for cutting data into intervals. Allows singleton intervals. Always includes the whole range of data by default. Flexible labelling. Convenience functions for cutting by quantiles etc. Handles dates, times, units and other vectors.

Maintained by David Hugh-Jones. Last updated 9 months ago.

cpp

5.7 match 138 stars 8.00 score 108 scripts 2 dependents

ropensci

rdflib:Tools to Manipulate and Query Semantic Data

The Resource Description Framework, or 'RDF' is a widely used data representation model that forms the cornerstone of the Semantic Web. 'RDF' represents data as a graph rather than the familiar data table or rectangle of relational databases. The 'rdflib' package provides a friendly and concise user interface for performing common tasks on 'RDF' data, such as reading, writing and converting between the various serializations of 'RDF' data, including 'rdfxml', 'turtle', 'nquads', 'ntriples', and 'json-ld'; creating new 'RDF' graphs, and performing graph queries using 'SPARQL'. This package wraps the low level 'redland' R package which provides direct bindings to the 'redland' C library. Additionally, the package supports the newer and more developer friendly 'JSON-LD' format through the 'jsonld' package. The package interface takes inspiration from the Python 'rdflib' library.

Maintained by Carl Boettiger. Last updated 7 months ago.

peer-reviewed

4.8 match 57 stars 9.59 score 123 scripts 7 dependents

ices-tools-prod

icesFO:Functions to support the creation of ICES Fisheries Overviews

Functions to support the creation of ICES Fisheries Overviews.

Maintained by Adriana Villamor. Last updated 9 months ago.

13.3 match 2 stars 3.41 score 260 scripts

openair-project

openair:Tools for the Analysis of Air Pollution Data

Tools to analyse, interpret and understand air pollution data. Data are typically regular time series and air quality measurement, meteorological data and dispersion model output can be analysed. The package is described in Carslaw and Ropkins (2012, <doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.

Maintained by David Carslaw. Last updated 25 days ago.

air-quality air-quality-data meteorology openair cpp

3.5 match 311 stars 12.91 score 1.2k scripts 12 dependents

christopherkenny

geomander:Geographic Tools for Studying Gerrymandering

A compilation of tools to complete common tasks for studying gerrymandering. This focuses on the geographic tool side of common problems, such as linking different levels of spatial units or estimating how to break up units. Functions exist for creating redistricting-focused data for the US.

Maintained by Christopher T. Kenny. Last updated 18 days ago.

cpp

5.8 match 14 stars 7.81 score 191 scripts 1 dependents

r-lib

clock:Date-Time Types and Tools

Provides a comprehensive library for date-time manipulations using a new family of orthogonal date-time classes (durations, time points, zoned-times, and calendars) that partition responsibilities so that the complexities of time zones are only considered when they are really needed. Capabilities include: date-time parsing, formatting, arithmetic, extraction and updating of components, and rounding.

Maintained by Davis Vaughan. Last updated 1 days ago.

cpp

3.1 match 106 stars 14.48 score 296 scripts 407 dependents

r-gregmisc

gtools:Various R Programming Tools

Functions to assist in R programming, including: - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse logit transformations ('logit', 'inv.logit'), - test if a value is missing, empty or contains only NA and NULL values ('invalid'), - manipulate R's .Last function ('addLast'), - define macros ('defmacro'), - detect odd and even integers ('odd', 'even'), - convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a binary search ('binsearch'), - sort strings containing both numeric and character components ('mixedsort'), - create a factor variable from the quantiles of a continuous variable ('quantcut'), - enumerate permutations and combinations ('combinations', 'permutation'), - calculate and convert between fold-change and log-ratio ('foldchange', 'logratio2foldchange', 'foldchange2logratio'), - calculate probabilities and generate random numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply a function over adjacent subsets of a vector ('running'), - modify the TCP_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of data frames, even if the column names don't match ('smartbind'), - generate significance stars from p-values ('stars.pval'), - convert characters to/from ASCII codes ('asc', 'chr'), - convert character vector to ASCII representation ('ASCIIfy'), - apply title capitalization rules to a character vector ('capwords').

Maintained by Ben Bolker. Last updated 9 months ago.

3.1 match 25 stars 14.47 score 11k scripts 1.1k dependents

r-lidar

rlas:Read and Write 'las' and 'laz' Binary File Formats Used for Remote Sensing Data

Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://www.asprs.org/divisions-committees/lidar-division/laser-las-file-format-exchange-activities>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.4 <https://laszip.org/>.

Maintained by Jean-Romain Roussel. Last updated 8 months ago.

asprs las laz lidar cpp

5.6 match 34 stars 8.03 score 49 scripts 9 dependents

bioc

RTCGAToolbox:A new tool for exporting TCGA Firehose data

Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.

Maintained by Marcel Ramos. Last updated 3 months ago.

differentialexpression geneexpression sequencing

4.6 match 18 stars 9.75 score 76 scripts 5 dependents

dfsp-spirit

pkgfilecache:Download and Manage Optional Package Data

Manage optional data for your package. The data can be hosted anywhere, and you have to give a Uniform Resource Locator (URL) for each file. File integrity checks are supported. This is useful for package authors who need to ship more than the 5 Megabyte of data currently allowed by the the Comprehensive R Archive Network (CRAN).

Maintained by Tim Schäfer. Last updated 1 years ago.

cache checksum developer-tools download files filestorage home-directory

7.5 match 7 stars 5.98 score 3 scripts 9 dependents

ai-sdc

acro:A Tool for Semi-Automating the Statistical Disclosure Control of Research Outputs

Assists researchers and output checkers by distinguishing between research output that is safe to publish, output that requires further analysis, and output that cannot be published because of substantial disclosure risk. A paper about the tool was presented at the UNECE Expert Meeting on Statistical Data Confidentiality 2023; see <https://uwe-repository.worktribe.com/output/11060964>.

Maintained by Jim Smith. Last updated 9 days ago.

data-privacy data-protection privacy privacy-tools statistical-disclosure-control statistical-software

10.8 match 1 stars 4.11 score 1 scripts

colinfay

attempt:Tools for Defensive Programming

Tools for defensive programming, inspired by 'purrr' mappers and based on 'rlang'.'attempt' extends and facilitates defensive programming by providing a consistent grammar, and provides a set of easy to use functions for common tests and conditions. 'attempt' only depends on 'rlang', and focuses on speed, so it can be easily integrated in other functions and used in data analysis.

Maintained by Colin Fay. Last updated 7 months ago.

3.8 match 126 stars 11.57 score 101 scripts 86 dependents

eblondel

rsdmx:Tools for Reading SDMX Data and Metadata

Set of classes and methods to read data and metadata documents exchanged through the Statistical Data and Metadata Exchange (SDMX) framework, currently focusing on the SDMX XML standard format (SDMX-ML).

Maintained by Emmanuel Blondel. Last updated 17 days ago.

api datastructures dsd read readsdmx sdmx sdmx-format sdmx-provider sdmx-standards statistics timeseries web-services

4.8 match 105 stars 9.22 score 4 dependents

oxfordihtm

codeditr:Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool

The World Health Organization's CoDEdit electronic tool is intended to help producers of cause-of-death statistics in strengthening their capacity to perform routine checks on their data. This package ports the original tool built using Microsoft Access into R so as to leverage the utility and function of the original tool into a usable application program interface that can be used for building more universal tools or for creating programmatic scientific workflows aimed at routine, automated, and large-scale monitoring of cause-of-death data.

Maintained by Ernest Guevarra. Last updated 3 months ago.

cod icd

9.5 match 3 stars 4.65 score 6 scripts

spatstat

spatstat.data:Datasets for 'spatstat' Family

Contains all the datasets for the 'spatstat' family of packages.

Maintained by Adrian Baddeley. Last updated 2 hours ago.

kernel-density point-process spatial-analysis spatial-data spatial-data-analysis spatstat statistical-analysis statistical-methods statistical-tests statistics

4.0 match 6 stars 11.00 score 186 scripts 228 dependents

ropengov

helsinki:R Tools for Helsinki Open Data

Tools for accessing various open data APIs in the Helsinki region in Finland. Current data sources include the Service Map API, Linked Events API, and Helsinki Region Infoshare statistics API.

Maintained by Juuso Parkkinen. Last updated 2 years ago.

ropengov finland helsinki helsinki-region

8.3 match 6 stars 5.28 score 21 scripts

kasperwelbers

RNewsflow:Tools for Comparing Text Messages Across Time and Media

A collection of tools for measuring the similarity of text messages and tracing the flow of messages over time and across media.

Maintained by Kasper Welbers. Last updated 12 months ago.

cpp

6.1 match 38 stars 7.15 score 31 scripts 2 dependents

bioc

APAlyzer:A toolkit for APA analysis using RNA-seq data

Perform 3'UTR APA, Intronic APA and gene expression analysis using RNA-seq data.

Maintained by Ruijia Wang. Last updated 5 months ago.

sequencing rnaseq differentialexpression geneexpression generegulation annotation dataimport software ative-polyadenylation bioinformatics-tool rna-seq

7.5 match 8 stars 5.81 score 9 scripts

emmanuelparadis

ape:Analyses of Phylogenetics and Evolution

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Maintained by Emmanuel Paradis. Last updated 1 months ago.

openblas cpp

2.5 match 64 stars 17.18 score 13k scripts 601 dependents

r-lib

cli:Helpers for Developing Command Line Interfaces

A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.

Maintained by Gábor Csárdi. Last updated 22 hours ago.

cli

2.2 match 664 stars 19.33 score 1.4k scripts 14k dependents

bioc

artMS:Analytical R tools for Mass Spectrometry

artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.

Maintained by David Jimenez-Morales. Last updated 5 months ago.

proteomics differentialexpression biomedicalinformatics systemsbiology massspectrometry annotation qualitycontrol genesetenrichment clustering normalization immunooncology multiplecomparison analysis analytical ap-ms bioconductor bioinformatics mass-spectrometry phosphoproteomics post-translational-modification quantitative-analysis

6.7 match 14 stars 6.41 score 13 scripts

rsquaredacademy

olsrr:Tools for Building OLS Regression Models

Tools designed to make it easier for users, particularly beginner/intermediate R users to build ordinary least squares regression models. Includes comprehensive regression output, heteroskedasticity tests, collinearity diagnostics, residual diagnostics, measures of influence, model fit assessment and variable selection procedures.

Maintained by Aravind Hebbali. Last updated 4 months ago.

collinearity-diagnostics linear-models regression stepwise-regression

3.5 match 103 stars 12.19 score 1.4k scripts 4 dependents

zheng206

ComBatFamQC:Comprehensive Batch Effect Diagnostics and Harmonization

Provides a comprehensive framework for batch effect diagnostics, harmonization, and post-harmonization downstream analysis. Features include interactive visualization tools, robust statistical tests, and a range of harmonization techniques. Additionally, 'ComBatFamQC' enables the creation of life-span age trend plots with estimated age-adjusted centiles and facilitates the generation of covariate-corrected residuals for analytical purposes. Methods for harmonization are based on approaches described in Johnson et al., (2007) <doi:10.1093/biostatistics/kxj037>, Beer et al., (2020) <doi:10.1016/j.neuroimage.2020.117129>, Pomponio et al., (2020) <doi:10.1016/j.neuroimage.2019.116450>, and Chen et al., (2021) <doi:10.1002/hbm.25688>.

Maintained by Zheng Ren. Last updated 2 months ago.

diagnostic-tool harmonization rshinyapp

8.0 match 2 stars 5.35 score 16 scripts

tidyverse

tibble:Simple Data Frames

Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the traditional data frame.

Maintained by Kirill Müller. Last updated 3 months ago.

tidy-data

1.9 match 693 stars 22.82 score 47k scripts 11k dependents

thinkr-open

lozen:Management tools for missions

Management tools for missions (internal and external). Includes weekly, GL projects, etc.

Maintained by Sébastien Rochette. Last updated 12 months ago.

experimental

7.9 match 7 stars 5.42 score 14 scripts

clementcalenge

adehabitatMA:Tools to Deal with Raster Maps

A collection of tools to deal with raster maps.

Maintained by Clement Calenge. Last updated 6 months ago.

6.7 match 1 stars 6.34 score 43 scripts 15 dependents

business-science

timetk:A Tool Kit for Working with Time Series

Easy visualization, wrangling, and feature engineering of time series data for forecasting and machine learning prediction. Consolidates and extends time series functionality from packages including 'dplyr', 'stats', 'xts', 'forecast', 'slider', 'padr', 'recipes', and 'rsample'.

Maintained by Matt Dancho. Last updated 1 years ago.

coercion coercion-functions data-mining dplyr forecast forecasting forecasting-models machine-learning series-decomposition series-signature tibble tidy tidyquant tidyverse time time-series timeseries

3.0 match 625 stars 14.15 score 4.0k scripts 16 dependents

netsimanalytics

NetSimR:Actuarial Functions for Non-Life Insurance Modelling

Assists actuaries and other insurance modellers in pricing, reserving and capital modelling for non-life insurance and reinsurance modelling. Provides functions that help model excess levels, capping and pure Incurred but not reported claims (pure IBNR). Includes capped mean, exposure curves and increased limit factor curves (ILFs) for LogNormal, Gamma, Pareto, Sliced LogNormal-Pareto and Sliced Gamma-Pareto distributions. Includes mean, probability density function (pdf), cumulative probability function (cdf) and inverse cumulative probability function for Sliced LogNormal-Pareto and Sliced Gamma-Pareto distributions. Includes calculating pure IBNR exposure with LogNormal and Gamma distribution for reporting delay. Includes three shiny tools, one to simulate insurance claims applying reinsurance structures, fit generalised linear models and fit claims frequency or severity distributions. Methods used in the package refer to Free for All by Yiannis Parizas (2023) <https://www.theactuary.com/2023/03/02/free-all>; Escaping the triangle by Yiannis Parizas (2019) <https://www.theactuary.com/features/2019/06/2019/06/05/escaping-triangle>; Take to excess by Yiannis Parizas (2019) <https://www.theactuary.com/features/2019/03/2019/03/06/taken-excess>.

Maintained by Yiannis Parizas. Last updated 1 years ago.

12.8 match 1 stars 3.33 score