Showing 200 of total 330 results (show query)
mhahsler
recommenderlab:Lab for Developing and Testing Recommender Algorithms
Provides a research infrastructure to develop and evaluate collaborative filtering recommender algorithms. This includes a sparse representation for user-item matrices, many popular algorithms, top-N recommendations, and cross-validation. Hahsler (2022) <doi:10.48550/arXiv.2205.12371>.
Maintained by Michael Hahsler. Last updated 7 months ago.
collaborative-filteringrecommender-system
32.9 match 214 stars 10.07 score 840 scripts 2 dependents
yixuan
recosystem:Recommender System using Matrix Factorization
R wrapper of the 'libmf' library <https://www.csie.ntu.edu.tw/~cjlin/libmf/> for recommender system using matrix factorization. It is typically used to approximate an incomplete matrix using the product of two matrices in a latent space. Other common names for this task include "collaborative filtering", "matrix completion", "matrix recovery", etc. High performance multi-core parallel computing is supported in this package.
Maintained by Yixuan Qiu. Last updated 2 years ago.
matrix-factorizationrecommender-systemcppopenmp
21.0 match 84 stars 7.97 score 101 scripts 6 dependents
hongooi73
SAR:Smart Adaptive Recommendations
'Smart Adaptive Recommendations' (SAR) is the name of a fast, scalable, adaptive algorithm for personalized recommendations based on user transactions and item descriptions. It produces easily explainable/interpretable recommendations and handles "cold item" and "semi-cold user" scenarios. This package provides two implementations of 'SAR': a standalone implementation, and an interface to a web service in Microsoft's 'Azure' cloud: <https://github.com/Microsoft/Product-Recommendations/blob/master/doc/sar.md>. The former allows fast and easy experimentation, and the latter provides robust scalability and extra features for production use.
Maintained by Hong Ooi. Last updated 4 years ago.
30.4 match 21 stars 5.32 score 20 scripts
ludovikcoba
rrecsys:Environment for Evaluating Recommender Systems
Processes standard recommendation datasets (e.g., a user-item rating matrix) as input and generates rating predictions and lists of recommended items. Standard algorithm implementations which are included in this package are the following: Global/Item/User-Average baselines, Weighted Slope One, Item-Based KNN, User-Based KNN, FunkSVD, BPR and weighted ALS. They can be assessed according to the standard offline evaluation methodology (Shani, et al. (2011) <doi:10.1007/978-0-387-85820-3_8>) for recommender systems using measures such as MAE, RMSE, Precision, Recall, F1, AUC, NDCG, RankScore and coverage measures. The package (Coba, et al.(2017) <doi: 10.1007/978-3-319-60042-0_36>) is intended for rapid prototyping of recommendation algorithms and education purposes.
Maintained by Ludovik Çoba. Last updated 3 years ago.
20.1 match 23 stars 6.84 score 25 scripts
david-cortes
recometrics:Evaluation Metrics for Implicit-Feedback Recommender Systems
Calculates evaluation metrics for implicit-feedback recommender systems that are based on low-rank matrix factorization models, given the fitted model matrices and data, thus allowing to compare models from a variety of libraries. Metrics include P@K (precision-at-k, for top-K recommendations), R@K (recall at k), AP@K (average precision at k), NDCG@K (normalized discounted cumulative gain at k), Hit@K (from which the 'Hit Rate' is calculated), RR@K (reciprocal rank at k, from which the 'MRR' or 'mean reciprocal rank' is calculated), ROC-AUC (area under the receiver-operating characteristic curve), and PR-AUC (area under the precision-recall curve). These are calculated on a per-user basis according to the ranking of items induced by the model, using efficient multi-threaded routines. Also provides functions for creating train-test splits for model fitting and evaluation.
Maintained by David Cortes. Last updated 2 months ago.
implicit-feedbackmatrix-factorizationrecommender-systemsopenblascppopenmp
17.7 match 28 stars 5.45 score
blue-matter
MSEtool:Management Strategy Evaluation Toolkit
Development, simulation testing, and implementation of management procedures for fisheries (see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Maintained by Adrian Hordyk. Last updated 26 days ago.
10.8 match 8 stars 7.69 score 163 scripts 3 dependents
openintrostat
openintro:Datasets and Supplemental Functions from 'OpenIntro' Textbooks and Labs
Supplemental functions and data for 'OpenIntro' resources, which includes open-source textbooks and resources for introductory statistics (<https://www.openintro.org/>). The package contains datasets used in our open-source textbooks along with custom plotting functions for reproducing book figures. Note that many functions and examples include color transparency; some plotting elements may not show up properly (or at all) when run in some versions of Windows operating system.
Maintained by Mine Çetinkaya-Rundel. Last updated 3 months ago.
7.2 match 240 stars 11.39 score 6.0k scripts
mlr-org
mlr3learners:Recommended Learners for 'mlr3'
Recommended Learners for 'mlr3'. Extends 'mlr3' with interfaces to essential machine learning packages on CRAN. This includes, but is not limited to: (penalized) linear and logistic regression, linear and quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support vector machines, and gradient boosting.
Maintained by Marc Becker. Last updated 4 months ago.
classificationlearnersmachine-learningmlr3regression
5.7 match 91 stars 11.51 score 1.5k scripts 10 dependents
ropensci
gigs:Assess Fetal, Newborn, and Child Growth with International Standards
Convert between anthropometric measures and z-scores/centiles in multiple growth standards, and classify fetal, newborn, and child growth accordingly. With a simple interface to growth standards from the World Health Organisation and International Fetal and Newborn Growth Consortium for the 21st Century, gigs makes growth assessment easy and reproducible for clinicians, researchers and policy-makers.
Maintained by Simon R Parker. Last updated 26 days ago.
anthropometrygrowth-standardsintergrowthwho
14.8 match 4 stars 4.38 score 8 scripts
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 5 days ago.
nixpeer-reviewedreproducibilityreproducible-research
6.0 match 235 stars 10.54 score 67 scriptsdavid-cortes
cmfrec:Collective Matrix Factorization for Recommender Systems
Collective matrix factorization (a.k.a. multi-view or multi-way factorization, Singh, Gordon, (2008) <doi:10.1145/1401890.1401969>) tries to approximate a (potentially very sparse or having many missing values) matrix 'X' as the product of two low-dimensional matrices, optionally aided with secondary information matrices about rows and/or columns of 'X', which are also factorized using the same latent components. The intended usage is for recommender systems, dimensionality reduction, and missing value imputation. Implements extensions of the original model (Cortes, (2018) <arXiv:1809.00366>) and can produce different factorizations such as the weighted 'implicit-feedback' model (Hu, Koren, Volinsky, (2008) <doi:10.1109/ICDM.2008.22>), the 'weighted-lambda-regularization' model, (Zhou, Wilkinson, Schreiber, Pan, (2008) <doi:10.1007/978-3-540-68880-8_32>), or the enhanced model with 'implicit features' (Rendle, Zhang, Koren, (2019) <arXiv:1905.01395>), with or without side information. Can use gradient-based procedures or alternating-least squares procedures (Koren, Bell, Volinsky, (2009) <doi:10.1109/MC.2009.263>), with either a Cholesky solver, a faster conjugate gradient solver (Takacs, Pilaszy, Tikk, (2011) <doi:10.1145/2043932.2043987>), or a non-negative coordinate descent solver (Franc, Hlavac, Navara, (2005) <doi:10.1007/11556121_50>), providing efficient methods for sparse and dense data, and mixtures thereof. Supports L1 and L2 regularization in the main models, offers alternative most-popular and content-based models, and implements functionality for cold-start recommendations and imputation of 2D data.
Maintained by David Cortes. Last updated 2 months ago.
cold-startcollaborative-filteringcollective-matrix-factorizationopenblasopenmp
9.0 match 120 stars 6.84 score 23 scripts
dmurdoch
rgl:3D Visualization Using OpenGL
Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Maintained by Duncan Murdoch. Last updated 2 months ago.
graphicsopenglrglwebgllibglulibglvndlibpnglibx11freetypecpp
3.5 match 91 stars 17.49 score 7.3k scripts 300 dependents
sooahnshin
aihuman:Experimental Evaluation of Algorithm-Assisted Human Decision-Making
Provides statistical methods for analyzing experimental evaluation of the causal impacts of algorithmic recommendations on human decisions developed by Imai, Jiang, Greiner, Halen, and Shin (2023) <doi:10.1093/jrsssa/qnad010> and Ben-Michael, Greiner, Huang, Imai, Jiang, and Shin (2024) <doi:10.48550/arXiv.2403.12108>. The data used for this paper, and made available here, are interim, based on only half of the observations in the study and (for those observations) only half of the study follow-up period. We use them only to illustrate methods, not to draw substantive conclusions.
Maintained by Sooahn Shin. Last updated 3 months ago.
13.3 match 2 stars 4.60 score 8 scripts
philchalmers
SimDesign:Structure for Organizing Monte Carlo Simulation Designs
Provides tools to safely and efficiently organize and execute Monte Carlo simulation experiments in R. The package controls the structure and back-end of Monte Carlo simulation experiments by utilizing a generate-analyse-summarise workflow. The workflow safeguards against common simulation coding issues, such as automatically re-simulating non-convergent results, prevents inadvertently overwriting simulation files, catches error and warning messages during execution, implicitly supports parallel processing with high-quality random number generation, and provides tools for managing high-performance computing (HPC) array jobs submitted to schedulers such as SLURM. For a pedagogical introduction to the package see Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Maintained by Phil Chalmers. Last updated 5 hours ago.
monte-carlo-simulationsimulationsimulation-framework
4.2 match 62 stars 13.38 score 253 scripts 46 dependents
kjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 11 months ago.
21.5 match 2.28 score 38 scripts
kosukeimai
MatchIt:Nonparametric Preprocessing for Parametric Causal Inference
Selects matched samples of the original treated and control groups with similar covariate distributions -- can be used to match exactly on covariates, to match on propensity scores, or perform a variety of other matching procedures. The package also implements a series of recommendations offered in Ho, Imai, King, and Stuart (2007) <DOI:10.1093/pan/mpl013>. (The 'gurobi' package, which is not on CRAN, is optional and comes with an installation of the Gurobi Optimizer, available at <https://www.gurobi.com>.)
Maintained by Noah Greifer. Last updated 2 days ago.
3.2 match 220 stars 15.03 score 2.4k scripts 21 dependents
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.
golemversehacktoberfestshinyshiny-appsshiny-rshinyapps
3.3 match 921 stars 14.23 score 167 scripts 62 dependents
dfsp-spirit
fsbrain:Managing and Visualizing Brain Surface Data
Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Maintained by Tim Schäfer. Last updated 4 months ago.
3dbraindtifreesurfermeshmrineuroimagingresearchsurfacevisualizationvoxel
7.1 match 66 stars 6.47 score 15 scripts
moderndive
moderndive:Tidyverse-Friendly Introductory Linear Regression
Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in "Statistical Inference via Data Science: A ModernDive into R and the Tidyverse" available at <https://moderndive.com/>.
Maintained by Albert Y. Kim. Last updated 3 months ago.
3.5 match 88 stars 11.35 score 1.8k scripts
chrisaberson
pwr2ppl:Power Analyses for Common Designs (Power to the People)
Statistical power analysis for designs including t-tests, correlations, multiple regression, ANOVA, mediation, and logistic regression. Functions accompany Aberson (2019) <doi:10.4324/9781315171500>.
Maintained by Chris Aberson. Last updated 3 years ago.
9.5 match 17 stars 4.16 score 17 scripts
agrocares
OBIC:Calculate the Open Bodem Index (OBI) Score
The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices. The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators. By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI. More information about the Open Bodem Index can be found at <https://openbodemindex.nl/>.
Maintained by Sven Verweij. Last updated 6 months ago.
5.6 match 11 stars 6.82 score 20 scripts
wviechtb
metafor:Meta-Analysis Package for R
A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit equal-, fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, bubble, and GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted. An introduction to the package can be found in Viechtbauer (2010) <doi:10.18637/jss.v036.i03>.
Maintained by Wolfgang Viechtbauer. Last updated 2 days ago.
meta-analysismixed-effectsmultilevel-modelsmultivariate
2.3 match 246 stars 16.30 score 4.9k scripts 92 dependents
bioc
biocViews:Categorized views of R package repositories
Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and 'experiment data' packages.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
infrastructurebioconductor-packagecore-package
3.7 match 4 stars 9.71 score 30 scripts 14 dependents
rstudio
gt:Easily Create Presentation-Ready Display Tables
Build display tables from tabular data with an easy-to-use set of functions. With its progressive approach, we can construct display tables with a cohesive set of table parts. Table values can be formatted using any of the included formatting functions. Footnotes and cell styles can be precisely added through a location targeting system. The way in which 'gt' handles things for you means that you don't often have to worry about the fine details.
Maintained by Richard Iannone. Last updated 12 days ago.
docxeasy-to-usehtmllatexrtfsummary-tables
1.8 match 2.1k stars 18.36 score 20k scripts 112 dependents
r-lib
gh:'GitHub' 'API'
Minimal client to access the 'GitHub' 'API'.
Maintained by Gábor Csárdi. Last updated 1 months ago.
2.0 match 224 stars 15.55 score 444 scripts 401 dependentsr-lib
lintr:A 'Linter' for R Code
Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual Studio Code'.
Maintained by Michael Chirico. Last updated 9 days ago.
1.8 match 1.2k stars 17.00 score 916 scripts 33 dependents
jwijffels
RMOA:Connect R with MOA for Massive Online Analysis
Connect R with MOA (Massive Online Analysis - <https://moa.cms.waikato.ac.nz/>) to build classification models and regression models on streaming data or out-of-RAM data. Also streaming recommendation models are made available.
Maintained by Jan Wijffels. Last updated 3 years ago.
11.3 match 1 stars 2.53 score 34 scripts
bnosac
ruimtehol:Learn Text 'Embeddings' with 'Starspace'
Wraps the 'StarSpace' library <https://github.com/facebookresearch/StarSpace> allowing users to calculate word, sentence, article, document, webpage, link and entity 'embeddings'. By using the 'embeddings', you can perform text based multi-label classification, find similarities between texts and categories, do collaborative-filtering based recommendation as well as content-based recommendation, find out relations between entities, calculate graph 'embeddings' as well as perform semi-supervised learning and multi-task learning on plain text. The techniques are explained in detail in the paper: 'StarSpace: Embed All The Things!' by Wu et al. (2017), available at <arXiv:1709.03856>.
Maintained by Jan Wijffels. Last updated 1 years ago.
classificationembeddingsnatural-language-processingnlpsimilaritystarspacetext-miningcpp
4.3 match 101 stars 6.65 score 44 scripts
r-quantities
constants:Reference on Constants, Units and Uncertainty
CODATA internationally recommended values of the fundamental physical constants, provided as symbols for direct use within the R language. Optionally, the values with uncertainties and/or units are also provided if the 'errors', 'units' and/or 'quantities' packages are installed. The Committee on Data for Science and Technology (CODATA) is an interdisciplinary committee of the International Council for Science which periodically provides the internationally accepted set of values of the fundamental physical constants. This package contains the "2018 CODATA" version, published on May 2019: Eite Tiesinga, Peter J. Mohr, David B. Newell, and Barry N. Taylor (2020) <https://physics.nist.gov/cuu/Constants/>.
Maintained by Iñaki Ucar. Last updated 2 years ago.
5.7 match 15 stars 4.78 score 27 scripts 1 dependents
frbcesab
rcompendium:Create a Package or Research Compendium Structure
Makes easier the creation of R package or research compendium (i.e. a predefined files/folders structure) so that users can focus on the code/analysis instead of wasting time organizing files. A full ready-to-work structure is set up with some additional features: version control, remote repository creation, CI/CD configuration (check package integrity under several OS, test code with 'testthat', and build and deploy website using 'pkgdown'). This package heavily relies on the R packages 'devtools' and 'usethis' and follows recommendations made by Wickham H. (2015) <ISBN:9781491910597> and Marwick B. et al. (2018) <doi:10.7287/peerj.preprints.3192v2>.
Maintained by Nicolas Casajus. Last updated 1 months ago.
reproducible-researchresearch-compendium
4.0 match 40 stars 6.72 score 22 scripts
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-analysisbayesian-statisticsdeveloper-toolsstan
2.0 match 50 stars 13.09 score 134 scripts 222 dependentsbioc
PureCN:Copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.
Maintained by Markus Riester. Last updated 2 months ago.
copynumbervariationsoftwaresequencingvariantannotationvariantdetectioncoverageimmunooncologybioconductor-packagecell-free-dnacopy-numberlohtumor-heterogeneitytumor-mutational-burdentumor-purity
2.7 match 132 stars 9.72 score 40 scripts
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 6 days ago.
1.3 match 584 stars 18.71 score 7.2k scripts 380 dependents
cran
datarobot:'DataRobot' Predictive Modeling API
For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Maintained by AJ Alon. Last updated 1 years ago.
7.1 match 2 stars 3.48 score
inbo
checklist:A Thorough and Strict Set of Checks for R Packages and Source Code
An opinionated set of rules for R packages and R source code projects.
Maintained by Thierry Onkelinx. Last updated 27 days ago.
checklistcontinuous-integrationcontinuous-testingquality-assurance
3.3 match 19 stars 7.24 score 21 scripts 2 dependents
rvlenth
emmeans:Estimated Marginal Means, aka Least-Squares Means
Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Maintained by Russell V. Lenth. Last updated 4 days ago.
1.3 match 377 stars 19.19 score 13k scripts 187 dependentsbioc
edgeR:Empirical Analysis of Digital Gene Expression Data in R
Differential expression analysis of sequence count data. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models, quasi-likelihood, and gene set enrichment. Can perform differential analyses of any type of omics data that produces read counts, including RNA-seq, ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral counts. RNA-seq analyses can be conducted at the gene or isoform level, and tests can be conducted for differential exon or transcript usage.
Maintained by Yunshun Chen. Last updated 6 days ago.
alternativesplicingbatcheffectbayesianbiomedicalinformaticscellbiologychipseqclusteringcoveragedifferentialexpressiondifferentialmethylationdifferentialsplicingdnamethylationepigeneticsfunctionalgenomicsgeneexpressiongenesetenrichmentgeneticsimmunooncologymultiplecomparisonnormalizationpathwaysproteomicsqualitycontrolregressionrnaseqsagesequencingsinglecellsystemsbiologytimecoursetranscriptiontranscriptomicsopenblas
1.7 match 13.40 score 17k scripts 255 dependents
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 10 days ago.
2.0 match 83 stars 11.39 score 2.1k scripts 8 dependents
wadpac
GGIR:Raw Accelerometer Data Analysis
A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.
Maintained by Vincent T van Hees. Last updated 3 days ago.
accelerometeractivity-recognitioncircadian-rhythmmovement-sensorsleep
1.7 match 109 stars 13.20 score 342 scripts 3 dependents
quanteda
quanteda:Quantitative Analysis of Textual Data
A fast, flexible, and comprehensive framework for quantitative text analysis in R. Provides functionality for corpus management, creating and manipulating tokens and n-grams, exploring keywords in context, forming and manipulating sparse matrices of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and distances, applying content dictionaries, applying supervised and unsupervised machine learning, visually representing text and text analyses, and more.
Maintained by Kenneth Benoit. Last updated 2 months ago.
corpusnatural-language-processingquantedatext-analyticsonetbbcpp
1.3 match 851 stars 16.68 score 5.4k scripts 51 dependentsmhahsler
recommenderlabJester:Jester Dataset for 'recommenderlab'
Provides the Jester Dataset for package recommenderlab.
Maintained by Michael Hahsler. Last updated 3 years ago.
7.5 match 2.70 score 1 scriptsmhahsler
recommenderlabBX:Book-Crossing Dataset (BX) for 'recommenderlab'
Provides the Book-Crossing Dataset for the package recommenderlab.
Maintained by Michael Hahsler. Last updated 3 years ago.
7.5 match 2.70 score 1 scriptsbioc
DESeq2:Differential gene expression analysis based on the negative binomial distribution
Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
Maintained by Michael Love. Last updated 12 days ago.
sequencingrnaseqchipseqgeneexpressiontranscriptionnormalizationdifferentialexpressionbayesianregressionprincipalcomponentclusteringimmunooncologyopenblascpp
1.3 match 375 stars 16.11 score 17k scripts 115 dependents
natverse
nat:NeuroAnatomy Toolbox for Analysis of 3D Image Data
NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Maintained by Gregory Jefferis. Last updated 5 months ago.
3dconnectomicsimage-analysisneuroanatomyneuroanatomy-toolboxneuronneuron-morphologyneurosciencevisualisation
2.0 match 67 stars 9.94 score 436 scripts 2 dependents
tscnlab
LightLogR:Process Data from Wearable Light Loggers and Optical Radiation Dosimeters
Import, processing, validation, and visualization of personal light exposure measurement data from wearable devices. The package implements features such as the import of data and metadata files, conversion of common file formats, validation of light logging data, verification of crucial metadata, calculation of common parameters, and semi-automated analysis and visualization.
Maintained by Johannes Zauner. Last updated 25 days ago.
dosimetrylighttime-series-analysiswearable-deviceswearable-sensors
3.3 match 12 stars 5.91 score 28 scripts
r-forge
Polychrome:Qualitative Palettes with Many Colors
Tools for creating, viewing, and assessing qualitative palettes with many (20-30 or more) colors. See Coombes and colleagues (2019) <doi:10.18637/jss.v090.c01>.
Maintained by Kevin R. Coombes. Last updated 1 months ago.
2.0 match 9.56 score 1.0k scripts 27 dependentsropensci
gutenbergr:Download and Process Public Domain Works from Project Gutenberg
Download and process public domain works in the Project Gutenberg collection <https://www.gutenberg.org/>. Includes metadata for all Project Gutenberg works, so that they can be searched and retrieved.
Maintained by Jon Harmon. Last updated 2 months ago.
1.8 match 105 stars 10.50 score 1.1k scripts 1 dependents
hughjonesd
rcheology:Data on Base and Recommended Packages for Current and Previous Versions of R
Provides a dataset of functions in all base and recommended packages of R versions 0.50 onwards.
Maintained by David Hugh-Jones. Last updated 14 days ago.
3.4 match 40 stars 5.56 score 9 scripts 1 dependentsbioc
omicsPrint:Cross omic genetic fingerprinting
omicsPrint provides functionality for cross omic genetic fingerprinting, for example, to verify sample relationships between multiple omics data types, i.e. genomic, transcriptomic and epigenetic (DNA methylation).
Maintained by Davy Cats. Last updated 5 months ago.
qualitycontrolgeneticsepigeneticstranscriptomicsdnamethylationtranscriptiongeneticvariabilityimmunooncology
3.5 match 5.20 score 32 scripts
tychelab
CoSMoS:Complete Stochastic Modelling Solution
Makes univariate, multivariate, or random fields simulations precise and simple. Just select the desired time series or random fields’ properties and it will do the rest. CoSMoS is based on the framework described in Papalexiou (2018, <doi:10.1016/j.advwatres.2018.02.013>), extended for random fields in Papalexiou and Serinaldi (2020, <doi:10.1029/2019WR026331>), and further advanced in Papalexiou et al. (2021, <doi:10.1029/2020WR029466>) to allow fine-scale space-time simulation of storms (or even cyclone-mimicking fields).
Maintained by Kevin Shook. Last updated 4 years ago.
2.5 match 11 stars 7.10 score 77 scripts
laresbernardo
lares:Analytics & Machine Learning Sidekick
Auxiliary package for better/faster analytics, visualization, data mining, and machine learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling, Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust results, without the need of repetitive coding or advanced R programming skills.
Maintained by Bernardo Lares. Last updated 25 days ago.
analyticsapiautomationautomldata-sciencedescriptive-statisticsh2omachine-learningmarketingmmmpredictive-modelingpuzzlerlanguagerobynvisualization
1.8 match 233 stars 9.84 score 185 scripts 1 dependentsr-lib
gitcreds:Query 'git' Credentials from 'R'
Query, set, delete credentials from the 'git' credential store. Manage 'GitHub' tokens and other 'git' credentials. This package is to be used by other packages that need to authenticate to 'GitHub' and/or other 'git' repositories.
Maintained by Gábor Csárdi. Last updated 7 months ago.
credentialscredentials-helpergitgithub
1.3 match 28 stars 13.28 score 372 scripts 405 dependents
oscarkjell
text:Analyses of Text using Transformers Models from HuggingFace, Natural Language Processing and Machine Learning
Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.
Maintained by Oscar Kjell. Last updated 4 days ago.
deep-learningmachine-learningnlptransformersopenjdk
1.3 match 146 stars 13.16 score 436 scripts 1 dependents
muschellij2
rscopus:Scopus Database 'API' Interface
Uses Elsevier 'Scopus' API <https://dev.elsevier.com/sc_apis.html> to download information about authors and their citations.
Maintained by John Muschelli. Last updated 1 years ago.
1.9 match 77 stars 9.33 score 124 scripts 3 dependents
brentkaplan
beezdemand:Behavioral Economic Easy Demand
Facilitates many of the analyses performed in studies of behavioral economic demand. The package supports commonly-used options for modeling operant demand including (1) data screening proposed by Stein, Koffarnus, Snider, Quisenberry, & Bickel (2015; <doi:10.1037/pha0000020>), (2) fitting models of demand such as linear (Hursh, Raslear, Bauman, & Black, 1989, <doi:10.1007/978-94-009-2470-3_22>), exponential (Hursh & Silberberg, 2008, <doi:10.1037/0033-295X.115.1.186>) and modified exponential (Koffarnus, Franck, Stein, & Bickel, 2015, <doi:10.1037/pha0000045>), and (3) calculating numerous measures relevant to applied behavioral economists (Intensity, Pmax, Omax). Also supports plotting and comparing data.
Maintained by Brent Kaplan. Last updated 7 months ago.
2.8 match 15 stars 6.12 score 29 scripts 1 dependentscran
thermocouple:Temperature Measurement with Thermocouples, RTD and IC Sensors
Temperature measurement data, equations and methods for thermocouples, wire RTD, thermistors, IC thermometers, bimetallic strips and the ITS-90.
Maintained by Jose Gama. Last updated 10 years ago.
10.0 match 1.68 score 48 scriptsbioc
crisprDesign:Comprehensive design of CRISPR gRNAs for nucleases and base editors
Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.
Maintained by Jean-Philippe Fortin. Last updated 12 days ago.
crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomics-analysisgrnagrna-sequencegrna-sequencessgrnasgrna-design
2.0 match 22 stars 8.28 score 80 scripts 3 dependents
kimberlywebb
COMBO:Correcting Misclassified Binary Outcomes in Association Studies
Use frequentist and Bayesian methods to estimate parameters from a binary outcome misclassification model. These methods correct for the problem of "label switching" by assuming that the sum of outcome sensitivity and specificity is at least 1. A description of the analysis methods is available in Hochstedler and Wells (2023) <doi:10.48550/arXiv.2303.10215>.
Maintained by Kimberly Hochstedler Webb. Last updated 20 days ago.
3.3 match 1 stars 5.08 score 4 scriptsbioc
sesame:SEnsible Step-wise Analysis of DNA MEthylation BeadChips
Tools For analyzing Illumina Infinium DNA methylation arrays. SeSAMe provides utilities to support analyses of multiple generations of Infinium DNA methylation BeadChips, including preprocessing, quality control, visualization and inference. SeSAMe features accurate detection calling, intelligent inference of ethnicity, sex and advanced quality control routines.
Maintained by Wanding Zhou. Last updated 2 months ago.
dnamethylationmethylationarraypreprocessingqualitycontrolbioinformaticsdna-methylationmicroarray
1.8 match 69 stars 9.08 score 258 scripts 1 dependents
darwin-eu
CodelistGenerator:Identify Relevant Clinical Codes and Evaluate Their Use
Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Maintained by Edward Burn. Last updated 26 days ago.
1.6 match 13 stars 9.87 score 165 scripts 4 dependents
rpolars
polars:Lightning-Fast 'DataFrame' Library
Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.
Maintained by Soren Welling. Last updated 4 days ago.
1.3 match 499 stars 12.01 score 1.0k scripts 2 dependents
ppbds
tutorial.helpers:Helper Functions for Creating Tutorials
Helper functions for creating, editing, and testing tutorials created with the 'learnr' package. Provides a simple method for allowing students to download their answers to tutorial questions. For examples of its use, see the 'r4ds.tutorials' package.
Maintained by David Kane. Last updated 5 days ago.
1.9 match 5 stars 8.48 score 152 scripts 1 dependents
gegznav
spAddins:RStudio Add-ins to Format R Markdown files (RETIRED PACKAGE)
The development of `spAddins` ended in 2018 as the package retired in favor of packages `addins.rmd` and `addins.rs`. ... RStudio Add-ins to Format Text and Insert Operators ... A set of RStudio addins that are designed to be used in combination with user-defined RStudio keyboard shortcuts. These addins either: 1) insert text at a cursor position (e.g. insert operators %>%, <<-, %$%, etc.), 2) replace symbols in selected pieces of text (e.g., convert backslashes to forward slashes which results in stings like "c:\data\" converted into "c:/data/") or 3) enclose text with special symbols (e.g., converts "bold" into "**bold**") which is convenient for editing R Markdown files.
Maintained by Vilmantas Gegzna. Last updated 4 years ago.
3.3 match 8 stars 4.60 score 8 scripts
dovinij
GxEprs:Genotype-by-Environment Interaction in Polygenic Score Models
A novel PRS model is introduced to enhance the prediction accuracy by utilising GxE effects. This package performs Genome Wide Association Studies (GWAS) and Genome Wide Environment Interaction Studies (GWEIS) using a discovery dataset. The package has the ability to obtain polygenic risk scores (PRSs) for a target sample. Finally it predicts the risk values of each individual in the target sample. Users have the choice of using existing models (Li et al., 2015) <doi:10.1093/annonc/mdu565>, (Pandis et al., 2013) <doi:10.1093/ejo/cjt054>, (Peyrot et al., 2018) <doi:10.1016/j.biopsych.2017.09.009> and (Song et al., 2022) <doi:10.1038/s41467-022-32407-9>, as well as newly proposed models for genomic risk prediction (refer to the URL for more details).
Maintained by Dovini Jayasinghe. Last updated 10 months ago.
4.6 match 2 stars 3.30 score
malaga-fca-group
fcaR:Formal Concept Analysis
Provides tools to perform fuzzy formal concept analysis, presented in Wille (1982) <doi:10.1007/978-3-642-01815-2_23> and in Ganter and Obiedkov (2016) <doi:10.1007/978-3-662-49291-8>. It provides functions to load and save a formal context, extract its concept lattice and implications. In addition, one can use the implications to compute semantic closures of fuzzy sets and, thus, build recommendation systems.
Maintained by Domingo Lopez Rodriguez. Last updated 2 years ago.
2.5 match 6 stars 6.02 score 70 scriptsropensci
spatsoc:Group Animal Relocation Data by Spatial and Temporal Relationship
Detects spatial and temporal groups in GPS relocations (Robitaille et al. (2019) <doi:10.1111/2041-210X.13215>). It can be used to convert GPS relocations to gambit-of-the-group format to build proximity-based social networks In addition, the randomizations function provides data-stream randomization methods suitable for GPS data.
Maintained by Alec L. Robitaille. Last updated 1 months ago.
1.5 match 24 stars 9.97 score 145 scripts 3 dependents
charlie86
spotifyr:R Wrapper for the 'Spotify' Web API
An R wrapper for pulling data from the 'Spotify' Web API <https://developer.spotify.com/documentation/web-api/> in bulk, or post items on a 'Spotify' user's playlist.
Maintained by Daniel Antal. Last updated 5 months ago.
music-information-retrievalspotify
1.8 match 374 stars 8.54 score 936 scripts
jessicakubrusly
CFilt:Recommendation by Collaborative Filtering
Provides methods and functions to implement a Recommendation System based on Collaborative Filtering Methodology. See Aggarwal (2016) <doi:10.1007/978-3-319-29659-3> for an overview.
Maintained by Jessica Kubrusly. Last updated 5 months ago.
14.9 match 1.00 score
zxw834
BayesianPlatformDesignTimeTrend:Simulate and Analyse Bayesian Platform Trial with Time Trend
Simulating the sequential multi-arm multi-stage or platform trial with Bayesian approach using the 'rstan' package, which provides the R interface for the Stan. This package supports fixed ratio and Bayesian adaptive randomization approaches for randomization. Additionally, it allows for the study of time trend problems in platform trials. There are demos available for a multi-arm multi-stage trial with two different null scenarios, as well as for Bayesian trial cutoff screening. The Bayesian adaptive randomisation approaches are described in: Trippa et al. (2012) <doi:10.1200/JCO.2011.39.8420> and Wathen et al. (2017) <doi:10.1177/1740774517692302>. The randomisation algorithm is described in: Zhao W <doi:10.1016/j.cct.2015.06.008>. The analysis methods of time trend effect in platform trial are described in: Saville et al. (2022) <doi:10.1177/17407745221112013> and Bofill Roig et al. (2022) <doi:10.1186/s12874-022-01683-w>.
Maintained by Ziyan Wang. Last updated 1 years ago.
analysisbayesian-adaptive-randomisationclinial-trialgroup-sequential-designsmultiarm-multistage-trialsplatform-trialssimulationcpp
3.4 match 4.38 score 12 scripts
mobiodiv
mobr:Measurement of Biodiversity
Functions for calculating metrics for the measurement biodiversity and its changes across scales, treatments, and gradients. The methods implemented in this package are described in: Chase, J.M., et al. (2018) <doi:10.1111/ele.13151>, McGlinn, D.J., et al. (2019) <doi:10.1111/2041-210X.13102>, McGlinn, D.J., et al. (2020) <doi:10.1101/851717>, and McGlinn, D.J., et al. (2023) <doi:10.1101/2023.09.19.558467>.
Maintained by Daniel McGlinn. Last updated 5 months ago.
biodiversityconservationecologyrarefactionspeciesstatistics
1.7 match 23 stars 8.59 score 93 scriptsbioc
geneRecommender:A gene recommender algorithm to identify genes coexpressed with a query set of genes
This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions.
Maintained by Greg Hather. Last updated 5 months ago.
4.4 match 3.30 score 1 scripts
albertoalmuinha
DSpoty:Get 'Spotify' API Multiple Information
'DSpoty' R package allows you to retrieve 'Spotify' API Information such as artists, albums, tracks, features tracks, recommendations or related artists. This package allows you to search all the information by name and also includes a distance based algorithm to find similar songs. More information: <https://developer.spotify.com/documentation/web-api/> .
Maintained by Alberto Almuiña. Last updated 5 years ago.
albumapiartist-informationmusicpopularity-artistspotify
4.4 match 4 stars 3.30 score
aidanmorales
rTwig:Realistic Quantitative Structure Models
Real Twig is a method to correct branch overestimation in quantitative structure models. Overestimated cylinders are correctly tapered using measured twig diameters of corresponding tree species. Supported quantitative structure modeling software includes 'TreeQSM', 'SimpleForest', 'Treegraph', and 'aRchi'. Also included is a novel database of twig diameters and tools for fractal analysis of point clouds.
Maintained by Aidan Morales. Last updated 14 days ago.
forestrylidarmodelingqsmrcppcpp
2.0 match 8 stars 7.10 score 13 scripts
johncoene
packer:An Opinionated Framework for Using 'JavaScript'
Enforces good practice and provides convenience functions to make work with 'JavaScript' not just easier but also scalable. It is a robust wrapper to 'NPM', 'yarn', and 'webpack' that enables to compartmentalize 'JavaScript' code, leverage 'NPM' and 'yarn' packages, include 'TypeScript', 'React', or 'Vue' in web applications, and much more.
Maintained by John Coene. Last updated 7 months ago.
2.3 match 148 stars 6.25 score 1 scripts 2 dependents
zdebruine
RcppML:Rcpp Machine Learning Library
Fast machine learning algorithms including matrix factorization and divisive clustering for large sparse and dense matrices.
Maintained by Zach DeBruine. Last updated 2 years ago.
clusteringmatrix-factorizationnmfrcpprcppeigensparse-matrixcppopenmp
1.3 match 104 stars 10.53 score 125 scripts 46 dependentsropensci
mapmetadata:Map health metadata onto predefined research domains
Prior to gaining full access to health datasets, explore publicly available metadata and map metadata onto predefined research domains. This package uses structural metadata files downloaded from the Health Data Research Gateway (https://healthdatagateway.org/en). In theory, any metadata file with the same structure as the files downloaded from this gateway can be used with this package, but the package has been developed and tested on metadata files from this gateway only.
Maintained by Rachael Stickland. Last updated 10 days ago.
hdrukhdruk-gatewayhealth-datametadatasail-databank
2.4 match 6 stars 5.86 score
di-laurabyrne
DImodelsMulti:Fit Multivariate Diversity-Interactions Models with Repeated Measures
An add-on package to 'DImodels' for the fitting of biodiversity and ecosystem function relationship study data with multiple ecosystem function responses and/or time points. This package uses the multivariate and repeated measures Diversity-Interactions (DI) methods developed by Kirwan et al. (2009) <doi:10.1890/08-1684.1>, Finn et al. (2013) <doi:10.1111/1365-2664.12041>, and Dooley et al. (2015) <doi:10.1111/ele.12504>.
Maintained by Laura Byrne. Last updated 9 months ago.
3.1 match 4.41 score 13 scripts
bioc
BANDITS:BANDITS: Bayesian ANalysis of DIfferenTial Splicing
BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.
Maintained by Simone Tiberi. Last updated 5 months ago.
differentialsplicingalternativesplicingbayesiangeneticsrnaseqsequencingdifferentialexpressiongeneexpressionmultiplecomparisonsoftwaretranscriptionstatisticalmethodvisualizationopenblascpp
2.3 match 17 stars 5.75 score 11 scripts 1 dependentsropensci
rredlist:'IUCN' Red List Client
'IUCN' Red List (<https://api.iucnredlist.org/>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.
Maintained by William Gearty. Last updated 1 months ago.
iucnbiodiversityapiweb-servicestraitshabitatspeciesconservationapi-wrapperiucn-red-listtaxize
1.2 match 53 stars 11.49 score 195 scripts 24 dependentsbioc
GRaNIE:GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data
Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have cell-type specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (GRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a GRN using single-cell or bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally (Capture) Hi-C data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach.
Maintained by Christian Arnold. Last updated 5 months ago.
softwaregeneexpressiongeneregulationnetworkinferencegenesetenrichmentbiomedicalinformaticsgeneticstranscriptomicsatacseqrnaseqgraphandnetworkregressiontranscriptionchipseq
2.5 match 5.40 score 24 scriptsbioc
POWSC:Simulation, power evaluation, and sample size recommendation for single cell RNA-seq
Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA-seq in the context of differential expression (DE), this topic in the field of single-cell RNA sequencing is understudied. Moreover, the unique data characteristics present in scRNA-seq such as sparsity and heterogeneity increase the challenge. We propose POWSC, a simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship.
Maintained by Kenong Su. Last updated 5 months ago.
differentialexpressionimmunooncologysinglecellsoftware
3.3 match 4.00 score 7 scripts
olink-proteomics
OlinkAnalyze:Facilitate Analysis of Proteomic Data from Olink
A collection of functions to facilitate analysis of proteomic data from Olink, primarily NPX data that has been exported from Olink Software. The functions also work on QUANT data from Olink by log- transforming the QUANT data. The functions are focused on reading data, facilitating data wrangling and quality control analysis, performing statistical analysis and generating figures to visualize the results of the statistical analysis. The goal of this package is to help users extract biological insights from proteomic data run on the Olink platform.
Maintained by Kathleen Nevola. Last updated 21 days ago.
olinkproteomicsproteomics-data-analysis
1.3 match 104 stars 9.72 score 61 scripts
jaredhuling
personalized:Estimation and Validation Methods for Subgroup Identification and Personalized Medicine
Provides functions for fitting and validation of models for subgroup identification and personalized medicine / precision medicine under the general subgroup identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>. This package is intended for use for both randomized controlled trials and observational studies and is described in detail in Huling and Yu (2021) <doi:10.18637/jss.v098.i05>.
Maintained by Jared Huling. Last updated 3 years ago.
causal-inferenceheterogeneity-of-treatment-effectindividualized-treatment-rulespersonalized-medicineprecision-medicinesubgroup-identificationtreatment-effectstreatment-scoring
1.7 match 32 stars 7.38 score 125 scripts 1 dependents
fcampelo
MOEADr:Component-Wise MOEA/D Implementation
Modular implementation of Multiobjective Evolutionary Algorithms based on Decomposition (MOEA/D) [Zhang and Li (2007), <DOI:10.1109/TEVC.2007.892759>] for quick assembling and testing of new algorithmic components, as well as easy replication of published MOEA/D proposals. The full framework is documented in a paper published in the Journal of Statistical Software [<doi:10.18637/jss.v092.i06>].
Maintained by Felipe Campelo. Last updated 2 years ago.
moeadmultiobjective-optimization
2.0 match 20 stars 6.30 score 40 scripts
kharchenkolab
pagoda2:Single Cell Analysis and Differential Expression
Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.
Maintained by Evan Biederstedt. Last updated 1 years ago.
scrna-seqsingle-cellsingle-cell-rna-seqtranscriptomicsopenblascppopenmp
1.6 match 222 stars 8.00 score 282 scripts
prodriguezsosa
conText:'a la Carte' on Text (ConText) Embedding Regression
A fast, flexible and transparent framework to estimate context-specific word and short document embeddings using the 'a la carte' embeddings approach developed by Khodak et al. (2018) <arXiv:1805.05388> and evaluate hypotheses about covariate effects on embeddings using the regression framework developed by Rodriguez et al. (2021)<https://github.com/prodriguezsosa/EmbeddingRegression>.
Maintained by Pedro L. Rodriguez. Last updated 11 months ago.
1.3 match 104 stars 9.40 score 1.7k scriptsdarwin-eu
DrugUtilisation:Summarise Patient-Level Drug Utilisation in Data Mapped to the OMOP Common Data Model
Summarise patient-level drug utilisation cohorts using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. New users and prevalent users cohorts can be generated and their characteristics, indication and drug use summarised.
Maintained by Martí Català. Last updated 2 months ago.
1.5 match 8.27 score 156 scripts 2 dependents
bschneidr
svrep:Tools for Creating, Updating, and Analyzing Survey Replicate Weights
Provides tools for creating and working with survey replicate weights, extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>. Implements bootstrap methods for complex surveys, including the generalized survey bootstrap as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>. Methods are provided for applying nonresponse adjustments to both full-sample and replicate weights as described by Rust and Rao (1996) <doi:10.1177/096228029600500305>. Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>. Diagnostic functions are included to compare weights and weighted estimates from different sets of replicate weights.
Maintained by Ben Schneider. Last updated 7 days ago.
1.5 match 8 stars 8.12 score 54 scripts 3 dependents
dieghernan
nominatimlite:Interface with 'Nominatim' API Service
Lite interface for getting data from 'OSM' service 'Nominatim' <https://nominatim.org/release-docs/latest/>. Extract coordinates from addresses, find places near a set of coordinates and return spatial objects on 'sf' format.
Maintained by Diego Hernangómez. Last updated 1 months ago.
geocodingopenstreetmapaddressnominatimreverse-geocodingshapefilespatialapi-wrapperapigis
1.5 match 20 stars 8.08 score 41 scripts 1 dependents
privefl
bigparallelr:Easy Parallel Tools
Utility functions for easy parallelism in R. Include some reexports from other packages, utility functions for splitting and parallelizing over blocks, and choosing and setting the number of cores used.
Maintained by Florian Privé. Last updated 5 months ago.
1.9 match 4 stars 6.44 score 76 scripts 19 dependents
carpentries
sandpaper:Create and Curate Carpentries Lessons
We provide tools to build a Carpentries-themed lesson repository into an accessible standalone static website. These include local tools and those designed to be used in a continuous integration context so that all the lesson author needs to focus on is writing the content of the actual lesson.
Maintained by Robert Davey. Last updated 2 months ago.
carpentriescarpentries-infrastructurecarpentries-workbenchlesson-templatelessonsmarkdownstatic-site-generator
1.5 match 44 stars 7.72 score 8 scriptskharchenkolab
conos:Clustering on Network of Samples
Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Maintained by Evan Biederstedt. Last updated 1 years ago.
batch-correctionscrna-seqsingle-cell-rna-seqopenblascppopenmp
1.6 match 204 stars 7.32 score 258 scripts
talegari
slimrec:Sparse Linear Method to Predict Ratings and Top-N Recommendations
Sparse Linear Method(SLIM) predicts ratings and top-n recommendations suited for sparse implicit positive feedback systems. SLIM is decomposed into multiple elasticnet optimization problems which are solved in parallel over multiple cores. The package is based on "SLIM: Sparse Linear Methods for Top-N Recommender Systems" by Xia Ning and George Karypis <doi:10.1109/ICDM.2011.134>.
Maintained by Srikanth KS. Last updated 8 years ago.
3.6 match 3 stars 3.18 score 6 scripts
hoxo-m
githubinstall:A Helpful Way to Install R Packages Hosted on GitHub
Provides an helpful way to install packages hosted on GitHub.
Maintained by Koji Makiyama. Last updated 7 years ago.
1.6 match 49 stars 7.29 score 177 scripts
lcbc-uio
tsdrtools:Convenience package for installing R-packages on UiO TSD
Some packages are hard to install on the secure closed server of the University of Oslo, TSD This package has some functions to help users more easily install packages to TSD that cannot be installed using the mini-CRAN service within TSD.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
2.7 match 6 stars 4.18 score 5 scripts
capro-uio
tsdrtools:Convenience package for installing R-packages on UiO TSD
Some packages are hard to install on the secure closed server of the University of Oslo, TSD This package has some functions to help users more easily install packages to TSD that cannot be installed using the mini-CRAN service within TSD.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
2.7 match 6 stars 4.18 score 5 scripts
leonawicz
lcars:LCARS Aesthetic for Shiny
Provides Shiny widgets and theme that support a 'Library Computer Access/Retrieval System' (LCARS) aesthetic for Shiny apps. The package also includes functions for adding a minimal LCARS theme to static 'ggplot2' graphs. More details about LCARS can be found at <https://en.wikipedia.org/wiki/LCARS>.
Maintained by Matthew Leonawicz. Last updated 6 months ago.
2.0 match 70 stars 5.54 score 9 scripts
rafael-ayala
NutrienTrackeR:Food Composition Information and Dietary Assessment
Provides a tool set for food information and dietary assessment. It uses food composition data from several reference databases, including: 'USDA' (United States), 'CIQUAL' (France), 'BEDCA' (Spain), 'CNF' (Canada) and 'STFCJ' (Japan). 'NutrienTrackeR' calculates the intake levels for both macronutrient and micronutrients, and compares them with the recommended dietary allowances (RDA). It includes a number of visualization tools, such as time series plots of nutrient intake, and pie-charts showing the main foods contributing to the intake level of a given nutrient. A shiny app exposing the main functionalities of the package is also provided.
Maintained by Rafael Ayala. Last updated 2 years ago.
5.0 match 2.18 score 15 scripts
nixtla
nixtlar:A Software Development Kit for 'Nixtla''s 'TimeGPT'
A Software Development Kit for working with 'Nixtla''s 'TimeGPT', a foundation model for time series forecasting. 'API' is an acronym for 'application programming interface'; this package allows users to interact with 'TimeGPT' via the 'API'. You can set and validate 'API' keys and generate forecasts via 'API' calls. It is compatible with 'tsibble' and base R. For more details visit <https://docs.nixtla.io/>.
Maintained by Mariana Menchero. Last updated 28 days ago.
1.3 match 30 stars 8.16 score 38 scripts
melissagwolf
dynamic:DFI Cutoffs for Latent Variable Models
Returns dynamic fit index (DFI) cutoffs for latent variable models that are tailored to the user's model statement, model type, and sample size. This is the counterpart of the Shiny Application, <https://dynamicfit.app>.
Maintained by Melissa G. Wolf. Last updated 2 months ago.
1.5 match 16 stars 7.13 score 139 scriptsbioc
CellNOptR:Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.
Maintained by Attila Gabor. Last updated 5 months ago.
cellbasedassayscellbiologyproteomicspathwaysnetworktimecourseimmunooncology
1.6 match 6.72 score 98 scripts 6 dependentsbioc
MPRAnalyze:Statistical Analysis of MPRA data
MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes.
Maintained by Tal Ashuach. Last updated 5 months ago.
immunooncologysoftwarestatisticalmethodsequencinggeneexpressioncellbiologycellbasedassaysdifferentialexpressionexperimentaldesignclassification
1.5 match 12 stars 6.86 score 30 scripts
pik-piam
mrland:MadRaT land data package
The package provides land related data via the madrat framework.
Maintained by Jan Philipp Dietrich. Last updated 10 days ago.
1.9 match 5.61 score 3 scripts 4 dependentsbioc
SPIAT:Spatial Image Analysis of Tissues
SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.
Maintained by Yuzhou Feng. Last updated 1 days ago.
biomedicalinformaticscellbiologyspatialclusteringdataimportimmunooncologyqualitycontrolsinglecellsoftwarevisualization
1.2 match 22 stars 8.59 score 69 scripts
jeroen
curl:A Modern and Flexible Web Client for R
Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.
Maintained by Jeroen Ooms. Last updated 23 days ago.
0.5 match 224 stars 19.98 score 4.0k scripts 5.9k dependents
ldavies99
afcolours:Government Analysis Function Recommended Accessible Colour Palette
Government Analysis Function recommended colours for use in charts on gov.uk to help meet accessibility guidance.
Maintained by Luke Davies. Last updated 2 years ago.
3.4 match 2.90 score 159 scriptsbioc
SpotClean:SpotClean adjusts for spot swapping in spatial transcriptomics data
SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.
Maintained by Zijian Ni. Last updated 5 months ago.
dataimportrnaseqsequencinggeneexpressionspatialsinglecelltranscriptomicspreprocessingrna-seqspatial-transcriptomics
1.5 match 28 stars 6.48 score 36 scripts
mvogel78
childsds:Data and Methods Around Reference Values in Pediatrics
Calculation of standard deviation scores and percentiles adduced from different standards (WHO, UK, Germany, Italy, China, etc). Also, references for laboratory values in children and adults are available, e.g., serum lipids, iron-related blood parameters, IGF, liver enzymes. See package documentation for full list.
Maintained by Mandy Vogel. Last updated 2 months ago.
3.4 match 2.83 score 51 scripts
uclahs-cds
CancerEvolutionVisualization:Publication Quality Phylogenetic Tree Plots
Generates tree plots with precise branch lengths, gene annotations, and cellular prevalence. The package handles complex tree structures (angles, lengths, etc.) and can be further refined as needed by the user.
Maintained by Paul Boutros. Last updated 2 days ago.
1.5 match 2 stars 6.34 score 5 scripts
mpiccirilli
Rlinkedin:Access to the LinkedIn API via R
A series of functions that allow users to access the 'LinkedIn' API to get information about connections, search for people and jobs, share updates with their network, and create group discussions. For more information about using the API please visit <https://developer.linkedin.com/>.
Maintained by Michael Piccirilli. Last updated 8 years ago.
1.9 match 86 stars 5.00 score 23 scripts
trackage
trip:Tracking Data
Access and manipulate spatial tracking data, with straightforward coercion from and to other formats. Filter for speed and create time spent maps from tracking data. There are coercion methods to convert between 'trip' and 'ltraj' from 'adehabitatLT', and between 'trip' and 'psp' and 'ppp' from 'spatstat'. Trip objects can be created from raw or grouped data frames, and from types in the 'sp', sf', 'amt', 'trackeR', 'mousetrap', and other packages, Sumner, MD (2011) <https://figshare.utas.edu.au/articles/thesis/The_tag_location_problem/23209538>.
Maintained by Michael D. Sumner. Last updated 8 months ago.
1.2 match 13 stars 7.72 score 137 scripts 1 dependents
crlsierra
SoilR:Models of Soil Organic Matter Decomposition
Functions for modeling Soil Organic Matter decomposition in terrestrial ecosystems with linear and nonlinear systems of differential equations. The package implements models according to the compartmental system representation described in Sierra and others (2012) <doi:10.5194/gmd-5-1045-2012> and Sierra and others (2014) <doi:10.5194/gmd-7-1919-2014>.
Maintained by Carlos A. Sierra. Last updated 1 years ago.
3.2 match 5 stars 2.88 score 153 scripts
safetygraphics
safetyGraphics:Interactive Graphics for Monitoring Clinical Trial Safety
A framework for evaluation of clinical trial safety. Users can interactively explore their data using the included 'Shiny' application.
Maintained by Jeremy Wildfire. Last updated 2 years ago.
1.1 match 98 stars 8.18 score 111 scriptsbioc
scCB2:CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
scCB2 is an R package implementing CB2 for distinguishing real cells from empty droplets in droplet-based single cell RNA-seq experiments (especially for 10x Chromium). It is based on clustering similar barcodes and calculating Monte-Carlo p-value for each cluster to test against background distribution. This cluster-level test outperforms single-barcode-level tests in dealing with low count barcodes and homogeneous sequencing library, while keeping FDR well controlled.
Maintained by Zijian Ni. Last updated 5 months ago.
dataimportrnaseqsinglecellsequencinggeneexpressiontranscriptomicspreprocessingclustering
1.7 match 10 stars 5.30 score 5 scripts
jcrodriguez1989
rco:The R Code Optimizer
Automatically apply different strategies to optimize R code. 'rco' functions take R code as input, and returns R code as output.
Maintained by Juan Cruz Rodriguez. Last updated 4 months ago.
compilerfastgcchpcoptimizationoptimizer
1.3 match 82 stars 6.73 score
seewooli
IRTest:Parameter Estimation of Item Response Theory with Estimation of Latent Distribution
Item response theory (IRT) parameter estimation using marginal maximum likelihood and expectation-maximization algorithm (Bock & Aitkin, 1981 <doi:10.1007/BF02293801>). Within parameter estimation algorithm, several methods for latent distribution estimation are available. Reflecting some features of the true latent distribution, these latent distribution estimation methods can possibly enhance the estimation accuracy and free the normality assumption on the latent distribution.
Maintained by Seewoo Li. Last updated 22 days ago.
1.7 match 2 stars 5.18 score 8 scripts
phil8192
obAnalytics:Limit Order Book Analytics
Data processing, visualisation and analysis of Limit Order Book event data.
Maintained by Philip Stubbings. Last updated 6 years ago.
bitcoinlimit-order-booktradingvisualisation
1.3 match 152 stars 6.36 score 30 scriptsdieghernan
arcgeocoder:Geocoding with the 'ArcGIS' REST API Service
Lite interface for finding locations of addresses or businesses around the world using the 'ArcGIS' REST API service <https://developers.arcgis.com/rest/geocode/api-reference/overview-world-geocoding-service.htm>. Address text can be converted to location candidates and a location can be converted into an address. No API key required.
Maintained by Diego Hernangómez. Last updated 1 months ago.
geocodingarcgisaddressreverse-geocodingapi-wrapperapi-restarcgis-apigis
1.5 match 2 stars 5.56 score 15 scriptsbioc
epiregulon:Gene regulatory network inference from single cell epigenomic data
Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.
Maintained by Xiaosai Yao. Last updated 7 days ago.
singlecellgeneregulationnetworkinferencenetworkgeneexpressiontranscriptiongenetargetcpp
1.3 match 14 stars 6.67 score 17 scripts
ausgis
GD:Geographical Detectors for Assessing Spatial Factors
Geographical detectors for measuring spatial stratified heterogeneity, as described in Jinfeng Wang (2010) <doi:10.1080/13658810802443457> and Jinfeng Wang (2016) <doi:10.1016/j.ecolind.2016.02.052>. Includes the optimal discretization of continuous data, four primary functions of geographical detectors, comparison of size effects of spatial unit and the visualizations of results. To use the package and to refer the descriptions of the package, methods and case datasets, please cite Yongze Song (2020) <doi:10.1080/15481603.2020.1760434>. The model has been applied in factor exploration of road performance and multi-scale spatial segmentation for network data, as described in Yongze Song (2018) <doi:10.3390/rs10111696> and Yongze Song (2020) <doi:10.1109/TITS.2020.3001193>, respectively.
Maintained by Wenbo Lv. Last updated 4 months ago.
geographical-detectorspatial-stratified-heterogeneity
1.1 match 13 stars 7.49 score 51 scriptscran
catalytic:Tools for Applying Catalytic Priors in Statistical Modeling
To improve estimation accuracy and stability in statistical modeling, catalytic prior distributions are employed, integrating observed data with synthetic data generated from a simpler model's predictive distribution. This approach enhances model robustness, stability, and flexibility in complex data scenarios. The catalytic prior distributions are introduced by 'Huang et al.' (2020, <doi:10.1073/pnas.1920913117>), Li and Huang (2023, <doi:10.48550/arXiv.2312.01411>).
Maintained by Dongming Huang. Last updated 3 months ago.
2.5 match 3.18 scorebioc
CaMutQC:An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations
CaMutQC is able to filter false positive mutations generated due to technical issues, as well as to select candidate cancer mutations through a series of well-structured functions by labeling mutations with various flags. And a detailed and vivid filter report will be offered after completing a whole filtration or selection section. Also, CaMutQC integrates serveral methods and gene panels for Tumor Mutational Burden (TMB) estimation.
Maintained by Xin Wang. Last updated 5 months ago.
softwarequalitycontrolgenetargetcancer-genomicssomatic-mutations
1.3 match 7 stars 5.92 score 1 scripts
klarsen1
MarketMatching:Market Matching and Causal Impact Inference
For a given test market find the best control markets using time series matching and analyze the impact of an intervention. The intervention could be a marketing event or some other local business tactic that is being tested. The workflow implemented in the Market Matching package utilizes dynamic time warping (the 'dtw' package) to do the matching and the 'CausalImpact' package to analyze the causal impact. In fact, this package can be considered a "workflow wrapper" for those two packages. In addition, if you don't have a chosen set of test markets to match, the Market Matching package can provide suggested test/control market pairs and pseudo prospective power analysis (measuring causal impact at fake interventions).
Maintained by Larsen Kim. Last updated 1 years ago.
1.1 match 132 stars 6.91 score 38 scripts
mdbrown
TreatmentSelection:Evaluate Treatment Selection Biomarkers
A suite of descriptive and inferential methods designed to evaluate one or more biomarkers for their ability to guide patient treatment recommendations. Package includes functions to assess the calibration of risk models; and plot, evaluate, and compare markers. Please see the reference Janes H, Brown MD, Huang Y, et al. (2014) <doi:10.1515/ijb-2012-0052> for further details.
Maintained by Marshall Brown. Last updated 8 years ago.
2.2 match 3 stars 3.62 score 14 scripts
matthiasgomolka
simfinapi:Accessing 'SimFin' Data
Through simfinapi, you can intuitively access the 'SimFin' Web-API (<https://www.simfin.com/>) to make 'SimFin' data easily available in R. To obtain an 'SimFin' API key (and thus to use this package), you need to register at <https://app.simfin.com/login>.
Maintained by Matthias Gomolka. Last updated 11 months ago.
1.3 match 19 stars 5.90 score 21 scripts
kopflab
ggstackplot:Create Overlapping Stacked Plots
Easily create overlapping grammar of graphics plots for scientific data visualization. This style of plotting is particularly common in climatology and oceanography research communities.
Maintained by Sebastian Kopf. Last updated 2 months ago.
1.8 match 2 stars 4.48 score
beniaminogreen
cragg:Tests for Weak Instruments in R
Implements Cragg-Donald (1993) <doi:10.1017/S0266466600007519> and Stock and Yogo (2005) <doi:10.1017/CBO9780511614491.006> tests for weak instruments in R.
Maintained by Beniamino Green. Last updated 4 years ago.
instrumental-variableivivreg2regressionweak-instruments
1.6 match 6 stars 4.76 score 19 scriptsbioc
BioCor:Functional similarities
Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships...
Maintained by Lluís Revilla Sancho. Last updated 5 months ago.
statisticalmethodclusteringgeneexpressionnetworkpathwaysnetworkenrichmentsystemsbiologybioconductor-packagesbioinformaticsfunctional-similaritygenegene-setspathway-analysissimilaritysimilarity-measurement
1.1 match 14 stars 6.59 score
anirban166
data.table.threads:Analyze Multi-Threading Performance for 'data.table' Functions
Assists in finding the most suitable thread count for the various 'data.table' routines that support parallel processing.
Maintained by Anirban Chetia. Last updated 3 months ago.
1.7 match 3 stars 4.35 score
alexpate30
rcprd:Extraction and Management of Clinical Practice Research Datalink Data
Simplify the process of extracting and processing Clinical Practice Research Datalink (CPRD) data in order to build datasets ready for statistical analysis. This process is difficult in 'R', as the raw data is very large and cannot be read into the R workspace. 'rcprd' utilises 'RSQLite' to create 'SQLite' databases which are stored on the hard disk. These are then queried to extract the required information for a cohort of interest, and create datasets ready for statistical analysis. The processes follow closely that from the 'rEHR' package, see Springate et al., (2017) <doi:10.1371/journal.pone.0171784>.
Maintained by Alexander Pate. Last updated 20 days ago.
1.3 match 2 stars 5.48 score 5 scripts
bioc
xCell2:A Tool for Generic Cell Type Enrichment Analysis
xCell2 provides methods for cell type enrichment analysis using cell type signatures. It includes three main functions - 1. xCell2Train for training custom references objects from bulk or single-cell RNA-seq datasets. 2. xCell2Analysis for conducting the cell type enrichment analysis using the custom reference. 3. xCell2GetLineage for identifying dependencies between different cell types using ontology.
Maintained by Almog Angel. Last updated 1 days ago.
geneexpressiontranscriptomicsmicroarrayrnaseqsinglecelldifferentialexpressionimmunooncologygenesetenrichment
1.2 match 6 stars 6.16 score 15 scripts
e-sensing
sits:Satellite Image Time Series Analysis for Earth Observation Data Cubes
An end-to-end toolkit for land use and land cover classification using big Earth observation data, based on machine learning methods applied to satellite image data cubes, as described in Simoes et al (2021) <doi:10.3390/rs13132428>. Builds regular data cubes from collections in AWS, Microsoft Planetary Computer, Brazil Data Cube, Copernicus Data Space Environment (CDSE), Digital Earth Africa, Digital Earth Australia, NASA HLS using the Spatio-temporal Asset Catalog (STAC) protocol (<https://stacspec.org/>) and the 'gdalcubes' R package developed by Appel and Pebesma (2019) <doi:10.3390/data4030092>. Supports visualization methods for images and time series and smoothing filters for dealing with noisy time series. Includes functions for quality assessment of training samples using self-organized maps as presented by Santos et al (2021) <doi:10.1016/j.isprsjprs.2021.04.014>. Includes methods to reduce training samples imbalance proposed by Chawla et al (2002) <doi:10.1613/jair.953>. Provides machine learning methods including support vector machines, random forests, extreme gradient boosting, multi-layer perceptrons, temporal convolutional neural networks proposed by Pelletier et al (2019) <doi:10.3390/rs11050523>, and temporal attention encoders by Garnot and Landrieu (2020) <doi:10.48550/arXiv.2007.00586>. Supports GPU processing of deep learning models using torch <https://torch.mlverse.org/>. Performs efficient classification of big Earth observation data cubes and includes functions for post-classification smoothing based on Bayesian inference as described by Camara et al (2024) <doi:10.3390/rs16234572>, and methods for active learning and uncertainty assessment. Supports region-based time series analysis using package supercells <https://jakubnowosad.com/supercells/>. Enables best practices for estimating area and assessing accuracy of land change as recommended by Olofsson et al (2014) <doi:10.1016/j.rse.2014.02.015>. Minimum recommended requirements: 16 GB RAM and 4 CPU dual-core.
Maintained by Gilberto Camara. Last updated 1 months ago.
big-earth-datacbersearth-observationeo-datacubesgeospatialimage-time-seriesland-cover-classificationlandsatplanetary-computerr-spatialremote-sensingrspatialsatellite-image-time-seriessatellite-imagerysentinel-2stac-apistac-catalogcpp
0.8 match 494 stars 9.50 score 384 scriptscapro-uio
nettskjemar:Connect to the 'nettskjema.no' API of the University of Oslo
Enables users to retrieve data, meta-data, and codebooks from <https://nettskjema.no/>. The data from the API is richer than from the online data portal. Mowinckel (2021) <doi:10.5281/zenodo.4745481>.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
1.5 match 2 stars 4.75 score 14 scripts
drodriguezperez
kselection:Selection of K in K-Means Clustering
Selection of k in k-means clustering based on Pham et al. paper ``Selection of k in k-means clustering''.
Maintained by Daniel Rodriguez. Last updated 3 years ago.
1.9 match 7 stars 3.69 score 14 scripts
watanabe-j
qfratio:Moments and Distributions of Ratios of Quadratic Forms Using Recursion
Evaluates moments of ratios (and products) of quadratic forms in normal variables, specifically using recursive algorithms developed by Bao and Kan (2013) <doi:10.1016/j.jmva.2013.03.002> and Hillier et al. (2014) <doi:10.1017/S0266466613000364>. Also provides distribution, quantile, and probability density functions of simple ratios of quadratic forms in normal variables with several algorithms. Originally developed as a supplement to Watanabe (2023) <doi:10.1007/s00285-023-01930-8> for evaluating average evolvability measures in evolutionary quantitative genetics, but can be used for a broader class of statistics. Generating functions for these moments are also closely related to the top-order zonal and invariant polynomials of matrix arguments.
Maintained by Junya Watanabe. Last updated 6 months ago.
quadratic-formsrcpprcppeigenzonal-polynomialscppopenmp
1.5 match 1 stars 4.60 score 5 scripts
pydemull
activAnalyzer:A 'Shiny' App to Analyze Accelerometer-Measured Daily Physical Behavior Data
A tool to analyse 'ActiGraph' accelerometer data and to implement the use of the PROactive Physical Activity in COPD (chronic obstructive pulmonary disease) instruments. Once analysis is completed, the app allows to export results to .csv files and to generate a report of the measurement. All the configured inputs relevant for interpreting the results are recorded in the report. In addition to the existing 'R' packages that are fully integrated with the app, the app uses some functions from the 'actigraph.sleepr' package developed by Petkova (2021) <https://github.com/dipetkov/actigraph.sleepr/>.
Maintained by Pierre-Yves de Müllenheim. Last updated 6 months ago.
accelerometeractigraphappmonitorshiny
1.3 match 5 stars 5.18 score 8 scriptsr-forge
tramnet:Penalized Transformation Models
Partially penalized versions of specific transformation models implemented in package 'mlt'. Available models include a fully parametric version of the Cox model, other parametric survival models (Weibull, etc.), models for binary and ordered categorical variables, normal and transformed-normal (Box-Cox type) linear models, and continuous outcome logistic regression. Hyperparameter tuning is facilitated through model-based optimization functionalities from package 'mlr3MBO'. The methodology is described in Kook et al. (2021) <doi:10.32614/RJ-2021-054>. Transformation models and model-based optimization are described in Hothorn et al. (2019) <doi:10.1111/sjos.12291> and Bischl et al. (2016) <arxiv:1703.03373>, respectively.
Maintained by Lucas Kook. Last updated 5 days ago.
1.7 match 4.12 score 2 scripts
nicwir
QurvE:Robust and User-Friendly Analysis of Growth and Fluorescence Curves
High-throughput analysis of growth curves and fluorescence data using three methods: linear regression, growth model fitting, and smooth spline fit. Analysis of dose-response relationships via smoothing splines or dose-response models. Complete data analysis workflows can be executed in a single step via user-friendly wrapper functions. The results of these workflows are summarized in detailed reports as well as intuitively navigable 'R' data containers. A 'shiny' application provides access to all features without requiring any programming knowledge. The package is described in further detail in Wirth et al. (2023) <doi:10.1038/s41596-023-00850-7>.
Maintained by Nicolas T. Wirth. Last updated 1 years ago.
1.1 match 25 stars 6.00 score 7 scripts
david-hammond
piecenorms:Calculate a Piecewise Normalised Score Using Class Intervals
Provides an implementation of piecewise normalisation techniques useful when dealing with the communication of skewed and highly skewed data. It also provides utilities that recommends a normalisation technique based on the distribution of the data.
Maintained by David Hammond. Last updated 8 months ago.
2.3 match 1 stars 3.00 score 3 scriptsbioc
PanomiR:Detection of miRNAs that regulate interacting groups of pathways
PanomiR is a package to detect miRNAs that target groups of pathways from gene expression data. This package provides functionality for generating pathway activity profiles, determining differentially activated pathways between user-specified conditions, determining clusters of pathways via the PCxN package, and generating miRNAs targeting clusters of pathways. These function can be used separately or sequentially to analyze RNA-Seq data.
Maintained by Pourya Naderi. Last updated 5 months ago.
geneexpressiongenesetenrichmentgenetargetmirnapathways
1.3 match 3 stars 4.89 score 13 scripts
kpagacz
tergo:Style Your Code Fast
Provides a set of functions that allow users for styling their R code according to the 'tidyverse' style guide. The package uses a native Rust implementation to ensure the highest performance. Learn more about 'tergo' at <https://rtergo.pagacz.io>.
Maintained by Konrad Pagacz. Last updated 30 days ago.
1.2 match 36 stars 5.56 score 3 scripts
pigian
janus:Optimized Recommending System Based on 'tensorflow'
Proposes a coarse-to-fine optimization of a recommending system based on deep-neural networks using 'tensorflow'.
Maintained by Giancarlo Vercellino. Last updated 2 years ago.
3.5 match 1.81 score 65 scripts
gcicc
figuRes2:Support for a Variety of Figure Production Tasks
We view a figure as a collection of graphs/tables assembled on a page and optionally annotated with metadata (titles, headers and footers). Functions and supporting documentation are offered to streamline a variety of figure production task.
Maintained by Greg Cicconetti. Last updated 3 years ago.
1.3 match 3 stars 4.78 score
burgette
OVtool:Omitted Variable Tool
This tool was designed to assess the sensitivity of research findings to omitted variables when estimating causal effects using propensity score (PS) weighting. This tool produces graphics and summary results that will enable a researcher to quantify the impact an omitted variable would have on their results. Burgette et al. (2021) describe the methodology behind the primary function in this package, ov_sim. The method is demonstrated in Griffin et al. (2020) <doi:10.1016/j.jsat.2020.108075>.
Maintained by Lane Burgette. Last updated 3 years ago.
2.3 match 2.78 score 12 scriptscran
RWsearch:Lazy Search in R Packages, Task Views, CRAN, the Web. All-in-One Download
Search by keywords in R packages, task views, CRAN, the web and display the results in the console or in txt, html or pdf files. Download the package documentation (html index, README, NEWS, pdf manual, vignettes, source code, binaries) with a single instruction. Visualize the package dependencies and CRAN checks. Compare the package versions, unload and install the packages and their dependencies in a safe order. Explore CRAN archives. Use the above functions for task view maintenance. Access web search engines from the console thanks to 80+ bookmarks. All functions accept standard and non-standard evaluation.
Maintained by Patrice Kiener. Last updated 4 days ago.
1.7 match 3.70 scorebioc
BadRegionFinder:BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.
Maintained by Sarah Sandmann. Last updated 2 months ago.
coveragesequencingalignmentwholegenomeclassification
1.8 match 3.60 score 1 scripts
marianschmidt
msSPChelpR:Helper Functions for Second Primary Cancer Analyses
A collection of helper functions for analyzing Second Primary Cancer data, including functions to reshape data, to calculate patient states and analyze cancer incidence.
Maintained by Marian Eberl. Last updated 1 years ago.
1.5 match 2 stars 4.18 score 15 scripts
nilspetras
IPV:Item Pool Visualization
Generate plots based on the Item Pool Visualization concept for latent constructs. Item Pool Visualizations are used to display the conceptual structure of a set of items (self-report or psychometric). Dantlgraber, Stieger, & Reips (2019) <doi:10.1177/2059799119884283>.
Maintained by Nils Petras. Last updated 2 years ago.
1.5 match 2 stars 4.00 score 3 scripts
hdarjus
exams.mylearn:Question Generation in the 'MyLearn' XML Format
Randomized multiple-select and single-select question generation for the 'MyLearn' teaching and learning platform. Question templates in the form of the R/exams package (see <http://www.r-exams.org/>) are transformed into XML format required by 'MyLearn'.
Maintained by Darjus Hosszejni. Last updated 4 years ago.
1.5 match 2 stars 4.00 score
temp20250212
MultiTraits:Analyzing and Visualizing Multidimensional Plant Traits
Implements analytical methods for multidimensional plant traits, including Competitors-Stress tolerators-Ruderals strategy analysis using leaf traits, Leaf-Height-Seed strategy analysis, Niche Periodicity Table analysis, and Trait Network analysis. Provides functions for data analysis, visualization, and network metrics calculation. Methods are based on Grime (1974) <doi:10.1038/250026a0>, Pierce et al. (2017) <doi:10.1111/1365-2435.12882>, Westoby (1998) <doi:10.1023/A:1004327224729>, Yang et al. (2022) <doi:10.1016/j.foreco.2022.120540>, Winemiller et al. (2015) <doi:10.1111/ele.12462>, He et al. (2020) <doi:10.1016/j.tree.2020.06.003>.
Maintained by Anonymous Author. Last updated 24 days ago.
1.5 match 3.90 score 16 scripts
luzhangstat
phase1PRMD:Personalized Repeated Measurement Design for Phase I Clinical Trials
Implements Bayesian phase I repeated measurement design that accounts for multidimensional toxicity endpoints and longitudinal efficacy measure from multiple treatment cycles. The package provides flags to fit a variety of model-based phase I design, including 1 stage models with or without individualized dose modification, 3-stage models with or without individualized dose modification, etc. Functions are provided to recommend dosage selection based on the data collected in the available patient cohorts and to simulate trial characteristics given design parameters. Yin, Jun, et al. (2017) <doi:10.1002/sim.7134>.
Maintained by Lu Zhang. Last updated 5 years ago.
2.1 match 2.74 score 11 scripts
bnaras
cubature:Adaptive Multivariate Integration over Hypercubes
R wrappers around the cubature C library of Steven G. Johnson for adaptive multivariate integration over hypercubes and the Cuba C library of Thomas Hahn for deterministic and Monte Carlo integration. Scalar and vector interfaces for cubature and Cuba routines are provided; the vector interfaces are highly recommended as demonstrated in the package vignette.
Maintained by Balasubramanian Narasimhan. Last updated 8 months ago.
0.5 match 12 stars 11.08 score 488 scripts 162 dependents
vinhdizzo
IRexamples:Collection of Practical Institutional Research Examples and Tutorials
Provides examples of code for analyzing data or accomplishing tasks that may be useful to institutional or educational researchers.
Maintained by Vinh Nguyen. Last updated 2 years ago.
1.1 match 4 stars 5.00 score 4 scripts
merliseclyde
BAS:Bayesian Variable Selection and Model Averaging using Bayesian Adaptive Sampling
Package for Bayesian Variable Selection and Model Averaging in linear models and generalized linear models using stochastic or deterministic sampling without replacement from posterior distributions. Prior distributions on coefficients are from Zellner's g-prior or mixtures of g-priors corresponding to the Zellner-Siow Cauchy Priors or the mixture of g-priors from Liang et al (2008) <DOI:10.1198/016214507000001337> for linear models or mixtures of g-priors from Li and Clyde (2019) <DOI:10.1080/01621459.2018.1469992> in generalized linear models. Other model selection criteria include AIC, BIC and Empirical Bayes estimates of g. Sampling probabilities may be updated based on the sampled models using sampling w/out replacement or an efficient MCMC algorithm which samples models using a tree structure of the model space as an efficient hash table. See Clyde, Ghosh and Littman (2010) <DOI:10.1198/jcgs.2010.09049> for details on the sampling algorithms. Uniform priors over all models or beta-binomial prior distributions on model size are allowed, and for large p truncated priors on the model space may be used to enforce sampling models that are full rank. The user may force variables to always be included in addition to imposing constraints that higher order interactions are included only if their parents are included in the model. This material is based upon work supported by the National Science Foundation under Division of Mathematical Sciences grant 1106891. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Maintained by Merlise Clyde. Last updated 4 months ago.
bayesianbayesian-inferencegeneralized-linear-modelslinear-regressionlogistic-regressionmcmcmodel-selectionpoisson-regressionpredictive-modelingregressionvariable-selectionfortranopenblas
0.5 match 44 stars 10.81 score 420 scripts 3 dependentsinbo
INBOmd:Markdown Templates for INBO
Several templates to generate reports, presentations and posters.
Maintained by Thierry Onkelinx. Last updated 1 years ago.
1.2 match 12 stars 4.52 score 11 scripts
kapelner
PTE:Personalized Treatment Evaluator
We provide inference for personalized medicine models. Namely, we answer the questions: (1) how much better does a purported personalized recommendation engine for treatments do over a business-as-usual approach and (2) is that difference statistically significant?
Maintained by Adam Kapelner. Last updated 6 years ago.
2.3 match 2.37 score 26 scripts
lechmadeyski
reproducer:Reproduce Statistical Analyses and Meta-Analyses
Includes data analysis and meta-analysis functions (e.g., to calculate effect sizes and 95% Confidence Intervals (CI) on Standardised Effect Sizes (d) for AB/BA cross-over repeated-measures experimental designs), data presentation functions (e.g., density curve overlaid on histogram),and the data sets analyzed in different research papers in software engineering (e.g., related to software defect prediction or multi- site experiment concerning the extent to which structured abstracts were clearer and more complete than conventional abstracts) to streamline reproducible research in software engineering.
Maintained by Lech Madeyski. Last updated 1 years ago.
1.5 match 3.50 score 63 scriptsinbo
forrescalc:Calculation of Aggregated Values on Dendrometry, Regeneration and Vegetation of Forests, Starting from Individual Tree Measures from Fieldmap
A collection of functions to load and aggregate measurements related to dendrometry, rejuvenation and vegetation, and to access plot level results from Flemish forest reserves in data package forresdat.
Maintained by Els Lommelen. Last updated 6 months ago.
1.3 match 3.79 score 123 scripts
cnuge
coil:Contextualization and Evaluation of COI-5P Barcode Data
Designed for the cleaning, contextualization and assessment of cytochrome c oxidase I DNA barcode data (COI-5P, or the five prime portion of COI). It contains functions for placing COI-5P barcode sequences into a common reading frame, translating DNA sequences to amino acids and for assessing the likelihood that a given barcode sequence includes an insertion or deletion error. The error assessment relies on the comparison of input sequences against nucleotide and amino acid profile hidden Markov models (PHMMs) (for details see Durbin et al. 1998, ISBN: 9780521629713) trained on a taxonomically diverse set of reference sequences. The functions are provided as a complete pipeline and are also available individually for efficient and targeted analysis of barcode data.
Maintained by Cameron M. Nugent. Last updated 1 years ago.
1.8 match 2.88 score 15 scripts
ly129
ktweedie:'Tweedie' Compound Poisson Model in the Reproducing Kernel Hilbert Space
Kernel-based 'Tweedie' compound Poisson gamma model using high-dimensional predictors for the analyses of zero-inflated response variables. The package features built-in estimation, prediction and cross-validation tools and supports choice of different kernel functions. For more details, please see Yi Lian, Archer Yi Yang, Boxiang Wang, Peng Shi & Robert William Platt (2023) <doi:10.1080/00401706.2022.2156615>.
Maintained by Yi Lian. Last updated 1 years ago.
1.3 match 2 stars 4.00 score 5 scripts
a2-ai
ghqc:Manage QC via GitHub Issues using Shiny Apps
This package launches 3 ghqc applications as background jobs to aid the QC process through the use of shiny apps. It also contains aides to maintain the proper setup of the ecosystem. Namely, it will aid in the installation of ghqc.app and its dependendencies into an isolated directory as to not interfere with the project being QCed.
Maintained by Wes Cummings. Last updated 1 months ago.
1.6 match 3.04 score 3 scriptscran
tRnslate:Translate R Code in Source Files
Evaluate inline or chunks of R code in template files and replace with their output modifying the resulting template.
Maintained by Mario A. Martinez Araya. Last updated 4 years ago.
2.0 match 2.48 score 1 dependents
philippallmann
modest:Model-Based Dose-Escalation Trials
User-friendly Shiny apps for designing and evaluating phase I cancer clinical trials, with the aim to estimate the maximum tolerated dose (MTD) of a novel drug, using a Bayesian decision procedure based on logistic regression.
Maintained by Philip Pallmann. Last updated 7 years ago.
1.5 match 1 stars 3.30 score 9 scripts
multimeric
HistDat:Summary Statistics for Histogram/Count Data
In some cases you will have data in a histogram format, where you have a vector of all possible observations, and a vector of how many times each observation appeared. You could expand this into a single 1D vector, but this may not be advisable if the counts are extremely large. 'HistDat' allows for the calculation of summary statistics without the need for expanding your data.
Maintained by Michael Milton. Last updated 4 years ago.
1.7 match 1 stars 3.00 score 7 scripts
jcval94
shortcuts:Useful Shortcuts to Interact with 'RStudio' Scripts
Integrates clipboard copied data in R Studio, loads and installs libraries within a R script and returns all valid arguments of a selected function.
Maintained by José Carlos Del Valle. Last updated 5 years ago.
1.6 match 2 stars 3.00 score 1 scriptsbioc
IntEREst:Intron-Exon Retention Estimator
This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).
Maintained by Ali Oghabian. Last updated 5 days ago.
softwarealternativesplicingcoveragedifferentialsplicingsequencingrnaseqalignmentnormalizationdifferentialexpressionimmunooncology
1.2 match 4.16 score 12 scripts
welch-lab
CytoSimplex:Simplex Visualization of Cell Fate Similarity in Single-Cell Data
Create simplex plots to visualize the similarity between single-cells and selected clusters in a 1-/2-/3-simplex space. Velocity information can be added as an additional layer. See Liu J, Wang Y et al (2023) <doi:10.1101/2023.12.07.570655> for more details.
Maintained by Yichen Wang. Last updated 6 months ago.
1.2 match 1 stars 4.00 score 3 scripts
qcrates
psidread:Streamline Building Panel Data from Panel Study of Income Dynamics ('PSID') Raw Files
Streamline the management, creation, and formatting of panel data from the Panel Study of Income Dynamics ('PSID') <https://psidonline.isr.umich.edu> using this user-friendly tool. Simply define variable names and input code book details directly from the 'PSID' official website, and this toolbox will efficiently facilitate the data preparation process, transforming raw 'PSID' files into a well-organized format ready for further analysis.
Maintained by Shuyi Qiu. Last updated 1 years ago.
1.3 match 1 stars 3.70 score 5 scripts
yoctozepto
MDFS:MultiDimensional Feature Selection
Functions for MultiDimensional Feature Selection (MDFS): calculating multidimensional information gains, scoring variables, finding important variables, plotting selection results. This package includes an optional CUDA implementation that speeds up information gain calculation using NVIDIA GPGPUs. R. Piliszek et al. (2019) <doi:10.32614/RJ-2019-019>.
Maintained by Radosław Piliszek. Last updated 3 months ago.
1.8 match 2.56 score 24 scripts 1 dependents
ugroempi
relaimpo:Relative Importance of Regressors in Linear Models
Provides several metrics for assessing relative importance in linear models. These can be printed, plotted and bootstrapped. The recommended metric is lmg, which provides a decomposition of the model explained variance into non-negative contributions. There is a version of this package available that additionally provides a new and also recommended metric called pmvd. If you are a non-US user, you can download this extended version from Ulrike Groempings web site.
Maintained by Ulrike Groemping. Last updated 1 years ago.
0.8 match 3 stars 5.75 score 632 scripts 3 dependents
rjdverse
RJDemetra:Interface to 'JDemetra+' Seasonal Adjustment Software
Interface around 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal adjustment software officially recommended to the members of the European Statistical System (ESS) and the European System of Central Banks. It offers full access to all options and outputs of 'JDemetra+', including the two leading seasonal adjustment methods TRAMO/SEATS+ and X-12ARIMA/X-13ARIMA-SEATS.
Maintained by Alain Quartier-la-Tente. Last updated 10 days ago.
0.5 match 53 stars 8.67 score 128 scripts 5 dependents
atmoschem
vein:Vehicular Emissions Inventories
Elaboration of vehicular emissions inventories, consisting in four stages, pre-processing activity data, preparing emissions factors, estimating the emissions and post-processing of emissions in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>. Before using VEIN you need to know the vehicular composition of your study area, in other words, the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to start with the project to download a template to create a structure of directories and scripts.
Maintained by Sergio Ibarra-Espinosa. Last updated 2 hours ago.
atmoschematmospheric-chemistryatmospheric-scienceatmospheric-sciencesemissionsemissions-modelvehicular-emissions-inventoriesveinfortranopenmp
0.5 match 46 stars 8.69 score 137 scripts
virgile-baudrot
morse:Modelling Reproduction and Survival Data in Ecotoxicology
Advanced methods for a valuable quantitative environmental risk assessment using Bayesian inference of survival and reproduction Data. Among others, it facilitates Bayesian inference of the general unified threshold model of survival (GUTS). See our companion paper Baudrot and Charles (2021) <doi:10.21105/joss.03200>, as well as complementary details in Baudrot et al. (2018) <doi:10.1021/acs.est.7b05464> and Delignette-Muller et al. (2017) <doi:10.1021/acs.est.6b05326>.
Maintained by Virgile Baudrot. Last updated 6 months ago.
1.3 match 3.26 score 60 scriptscran
tmplate:Code Generation Based on Templates
Define general templates with tags that can be replaced by content depending on arguments and objects to modify the final output of the document.
Maintained by Mario A. Martinez Araya. Last updated 4 years ago.
2.0 match 2.00 score 5 scripts
scottkosty
bootstrap:Functions for the Book "An Introduction to the Bootstrap"
Software (bootstrap, cross-validation, jackknife) and data for the book "An Introduction to the Bootstrap" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. This package is primarily provided for projects already based on it, and for support of the book. New projects should preferentially use the recommended package "boot".
Maintained by Scott Kostyshak. Last updated 6 years ago.
0.5 match 7.62 score 890 scripts 30 dependentscran
gsrs:A Group-Specific Recommendation System
A group-specific recommendation system to use dependency information from users and items which share similar characteristics under the singular value decomposition framework. Refer to paper A Group-Specific Recommender System <doi:10.1080/01621459.2016.1219261> for the details.
Maintained by Yifei Zhang. Last updated 4 years ago.
3.9 match 1.00 scoreropensci
tiler:Create Geographic and Non-Geographic Map Tiles
Creates geographic map tiles from geospatial map files or non-geographic map tiles from simple image files. This package provides a tile generator function for creating map tile sets for use with packages such as 'leaflet'. In addition to generating map tiles based on a common raster layer source, it also handles the non-geographic edge case, producing map tiles from arbitrary images. These map tiles, which have a non-geographic, simple coordinate reference system (CRS), can also be used with 'leaflet' when applying the simple CRS option. Map tiles can be created from an input file with any of the following extensions: tif, grd and nc for spatial maps and png, jpg and bmp for basic images. This package requires 'Python' and the 'gdal' library for 'Python'. 'Windows' users are recommended to install 'OSGeo4W' (<https://trac.osgeo.org/osgeo4w/>) as an easy way to obtain the required 'gdal' support for 'Python'.
Maintained by Matthew Leonawicz. Last updated 6 months ago.
0.5 match 64 stars 7.78 score 39 scripts 2 dependents
rmhogervorst
pinboardr:Get information from 'pinboard.in' API
Full connectivity to the 'pinboard.in' service. Retrieve bookmarks, add new ones. Add, delete and rename tags, all from the convenience of your R session.
Maintained by Roel M. Hogervorst. Last updated 5 years ago.
1.7 match 4 stars 2.30 score 7 scripts
dusadrian
admisc:Adrian Dusa's Miscellaneous
Contains functions used across packages 'DDIwR', 'QCA' and 'venn'. Interprets and translates, factorizes and negates SOP - Sum of Products expressions, for both binary and multi-value crisp sets, and extracts information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly versatile recoding routine and some more flexible alternatives to the base functions 'with()' and 'within()'. SOP simplification functions in this package use related minimization from package 'QCA', which is recommended to be installed despite not being listed in the Imports field, due to circular dependency issues.
Maintained by Adrian Dusa. Last updated 4 days ago.
0.5 match 2 stars 7.61 score 20 scripts 92 dependents
ctu-bern
presize:Precision Based Sample Size Calculation
Bland (2009) <doi:10.1136/bmj.b3985> recommended to base study sizes on the width of the confidence interval rather the power of a statistical test. The goal of 'presize' is to provide functions for such precision based sample size calculations. For a given sample size, the functions will return the precision (width of the confidence interval), and vice versa.
Maintained by Alan G. Haynes. Last updated 5 months ago.
confidence-intervalsprecisionsample-size-calculationshiny-app
0.5 match 17 stars 7.22 score 36 scripts 1 dependents
ggpmxdevelopment
ggPMX:'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models
At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling activities in order to reduce the overall effort required for generating such plots. For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox, called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient for publication and submissions using few lines of code. This package focuses on plots recommended by ISoP <doi:10.1002/psp4.12161>. While not required, you can get/install the 'R' 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>. When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required Chart Data instead of exporting it from the 'Monolix' gui.
Maintained by Matthew Fidler. Last updated 1 years ago.
0.5 match 39 stars 7.23 score 80 scripts
jbgruber
LexisNexisTools:Working with Files from 'LexisNexis'
My PhD supervisor once told me that everyone doing newspaper analysis starts by writing code to read in files from the 'LexisNexis' newspaper archive (retrieved e.g., from <https://www.lexisnexis.com/> or any of the partner sites). However, while this is a nice exercise I do recommend, not everyone has the time. This package takes files downloaded from the newspaper archive of 'LexisNexis', reads them into R and offers functions for further processing.
Maintained by Johannes B. Gruber. Last updated 11 months ago.
0.5 match 107 stars 7.14 score 65 scripts
randy3k
iterpc:Efficient Iterator for Permutations and Combinations
Iterator for generating permutations and combinations. They can be either drawn with or without replacement, or with distinct/ non-distinct items (multiset). The generated sequences are in lexicographical order (dictionary order). The algorithms to generate permutations and combinations are memory efficient. These iterative algorithms enable users to process all sequences without putting all results in the memory at the same time. The algorithms are written in C/C++ for faster performance. Note: 'iterpc' is no longer being maintained. Users are recommended to switch to 'arrangements'.
Maintained by Randy Lai. Last updated 5 years ago.
0.5 match 9 stars 7.17 score 47 scripts 5 dependents
bioc
Rbowtie:R bowtie wrapper
This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.
Maintained by Michael Stadler. Last updated 2 months ago.
0.5 match 1 stars 6.80 score 22 scripts 8 dependents
bcjaeger
PooledCohort:Predicted Risk for CVD using Pooled Cohort Equations, PREVENT Equations, and Other Contemporary CVD Risk Calculators
The 2017 American College of Cardiology and American Heart Association blood pressure guideline recommends using 10-year predicted atherosclerotic cardiovascular disease risk to guide the decision to initiate or intensify antihypertensive medication. The guideline recommends using the Pooled Cohort risk prediction equations to predict 10-year atherosclerotic cardiovascular disease risk. This package implements the original Pooled Cohort risk prediction equations and also incorporates updated versions based on more contemporary data and statistical methods.
Maintained by Byron Jaeger. Last updated 6 months ago.
0.8 match 7 stars 4.50 score 8 scripts 1 dependents