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tidymodels

infer:Tidy Statistical Inference

The objective of this package is to perform inference using an expressive statistical grammar that coheres with the tidy design framework.

Maintained by Simon Couch. Last updated 6 months ago.

736 stars 15.75 score 3.5k scripts 18 dependents

r-lib

generics:Common S3 Generics not Provided by Base R Methods Related to Model Fitting

In order to reduce potential package dependencies and conflicts, generics provides a number of commonly used S3 generics.

Maintained by Hadley Wickham. Last updated 1 years ago.

61 stars 14.00 score 131 scripts 9.8k dependents

bhklab

mRMRe:Parallelized Minimum Redundancy, Maximum Relevance (mRMR)

Computes mutual information matrices from continuous, categorical and survival variables, as well as feature selection with minimum redundancy, maximum relevance (mRMR) and a new ensemble mRMR technique. Published in De Jay et al. (2013) <doi:10.1093/bioinformatics/btt383>.

Maintained by Benjamin Haibe-Kains. Last updated 4 years ago.

cppopenmp

19 stars 8.95 score 105 scripts 2 dependents

radiant-rstats

radiant.data:Data Menu for Radiant: Business Analytics using R and Shiny

The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.

Maintained by Vincent Nijs. Last updated 5 months ago.

53 stars 8.25 score 146 scripts 6 dependents

ekstroem

dataMaid:A Suite of Checks for Identification of Potential Errors in a Data Frame as Part of the Data Screening Process

Data screening is an important first step of any statistical analysis. dataMaid auto generates a customizable data report with a thorough summary of the checks and the results that a human can use to identify possible errors. It provides an extendable suite of test for common potential errors in a dataset.

Maintained by Claus Thorn Ekstrøm. Last updated 3 years ago.

data-cleaningdata-screeningreproducible-research

143 stars 7.53 score 236 scripts

matrix-profile-foundation

tsmp:Time Series with Matrix Profile

A toolkit implementing the Matrix Profile concept that was created by CS-UCR <http://www.cs.ucr.edu/~eamonn/MatrixProfile.html>.

Maintained by Francisco Bischoff. Last updated 3 years ago.

algorithmmatrix-profilemotif-searchtime-seriescpp

72 stars 7.29 score 179 scripts 1 dependents

joon-e

tidycomm:Data Modification and Analysis for Communication Research

Provides convenience functions for common data modification and analysis tasks in communication research. This includes functions for univariate and bivariate data analysis, index generation and reliability computation, and intercoder reliability tests. All functions follow the style and syntax of the tidyverse, and are construed to perform their computations on multiple variables at once. Functions for univariate and bivariate data analysis comprise summary statistics for continuous and categorical variables, as well as several tests of bivariate association including effect sizes. Functions for data modification comprise index generation and automated reliability analysis of index variables. Functions for intercoder reliability comprise tests of several intercoder reliability estimates, including simple and mean pairwise percent agreement, Krippendorff's Alpha (Krippendorff 2004, ISBN: 9780761915454), and various Kappa coefficients (Brennan & Prediger 1981 <doi: 10.1177/001316448104100307>; Cohen 1960 <doi: 10.1177/001316446002000104>; Fleiss 1971 <doi: 10.1037/h0031619>).

Maintained by Julian Unkel. Last updated 11 months ago.

15 stars 6.59 score 52 scripts

ropensci

coder:Deterministic Categorization of Items Based on External Code Data

Fast categorization of items based on external code data identified by regular expressions. A typical use case considers patient with medically coded data, such as codes from the International Classification of Diseases ('ICD') or the Anatomic Therapeutic Chemical ('ATC') classification system. Functions of the package relies on a triad of objects: (1) case data with unit id:s and possible dates of interest; (2) external code data for corresponding units in (1) and with optional dates of interest and; (3) a classification scheme ('classcodes' object) with regular expressions to identify and categorize relevant codes from (2). It is easy to introduce new classification schemes ('classcodes' objects) or to use default schemes included in the package. Use cases includes patient categorization based on 'comorbidity indices' such as 'Charlson', 'Elixhauser', 'RxRisk V', or the 'comorbidity-polypharmacy' score (CPS), as well as adverse events after hip and knee replacement surgery.

Maintained by Erik Bulow. Last updated 2 years ago.

classificationicd-10

22 stars 6.31 score 23 scripts

bioc

RCX:R package implementing the Cytoscape Exchange (CX) format

Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.

Maintained by Florian Auer. Last updated 5 months ago.

pathwaysdataimportnetwork

8 stars 6.28 score 10 scripts 1 dependents

ekstroem

dataReporter:Reproducible Data Screening Checks and Report of Possible Errors

Data screening is an important first step of any statistical analysis. 'dataReporter' auto generates a customizable data report with a thorough summary of the checks and the results that a human can use to identify possible errors. It provides an extendable suite of test for common potential errors in a dataset. See Petersen AH, Ekstrøm CT (2019). "dataMaid: Your Assistant for Documenting Supervised Data Quality Screening in R." _Journal of Statistical Software_, *90*(6), 1-38 <doi:10.18637/jss.v090.i06> for more information.

Maintained by Claus Thorn Ekstrøm. Last updated 2 years ago.

86 stars 6.16 score 34 scripts

mcanouil

NACHO:NanoString Quality Control Dashboard

NanoString nCounter data are gene expression assays where there is no need for the use of enzymes or amplification protocols and work with fluorescent barcodes (Geiss et al. (2018) <doi:10.1038/nbt1385>). Each barcode is assigned a messenger-RNA/micro-RNA (mRNA/miRNA) which after bonding with its target can be counted. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA. 'NACHO' (NAnoString quality Control dasHbOard) is able to analyse the exported NanoString nCounter data and facilitates the user in performing a quality control. 'NACHO' does this by visualising quality control metrics, expression of control genes, principal components and sample specific size factors in an interactive web application.

Maintained by Mickaël Canouil. Last updated 1 years ago.

mirnamrnananostringnormalisationquality-controlshiny

8 stars 5.41 score 32 scripts

maxwestphal

cases:Stratified Evaluation of Subgroup Classification Accuracy

Enables simultaneous statistical inference for the accuracy of multiple classifiers in multiple subgroups (strata). For instance, allows to perform multiple comparisons in diagnostic accuracy studies with co-primary endpoints sensitivity and specificity (Westphal M, Zapf A. Statistical inference for diagnostic test accuracy studies with multiple comparisons. Statistical Methods in Medical Research. 2024;0(0). <doi:10.1177/09622802241236933>).

Maintained by Max Westphal. Last updated 3 months ago.

1 stars 4.59 score 13 scripts

discoleo

Rpdb:Read, Write, Visualize and Manipulate PDB Files

Provides tools to read, write, visualize Protein Data Bank (PDB) files and perform some structural manipulations.

Maintained by Leonard Mada. Last updated 9 days ago.

4.53 score 68 scripts

bioc

MethylAid:Visual and interactive quality control of large Illumina DNA Methylation array data sets

A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.

Maintained by L.J.Sinke. Last updated 5 months ago.

dnamethylationmethylationarraymicroarraytwochannelqualitycontrolbatcheffectvisualizationgui

4.51 score 16 scripts

fvafrcu

fakemake:Mock the Unix Make Utility

Use R as a minimal build system. This might come in handy if you are developing R packages and can not use a proper build system. Stay away if you can (use a proper build system).

Maintained by Andreas Dominik Cullmann. Last updated 2 years ago.

4.22 score 11 scripts 1 dependents

mikeasilva

simplegraphdb:A Simple Graph Database

This is a graph database in 'SQLite'. It is inspired by Denis Papathanasiou's Python simple-graph project on 'GitHub'.

Maintained by Michael Silva. Last updated 4 years ago.

graphsqlitesqlite-database

7 stars 3.75 score 16 scripts

jroberayalas

ahnr:An Implementation of the Artificial Hydrocarbon Networks

Implementation of the Artificial Hydrocarbon Networks for data modeling.

Maintained by Jose Roberto Ayala Solares. Last updated 7 years ago.

1 stars 3.70 score 6 scripts

muhlisoz

dematel:Decision Making Trial and Evaluation Laboratory Technique in R

Developed to Solve the Multi-Criteria Decision Making Problems with Decision Making Trial and Evaluation Laboratory Technique in R.

Maintained by Muhlis Ozdemir. Last updated 4 years ago.

1 stars 2.00 score 2 scripts

cran

sbw:Stable Balancing Weights for Causal Inference and Missing Data

Implements the Stable Balancing Weights by Zubizarreta (2015) <DOI:10.1080/01621459.2015.1023805>. These are the weights of minimum variance that approximately balance the empirical distribution of the observed covariates. For an overview, see Chattopadhyay, Hase and Zubizarreta (2020) <DOI:10.1002/sim.8659>. To solve the optimization problem in 'sbw', the default solver is 'quadprog', which is readily available through CRAN. The solver 'osqp' is also posted on CRAN. To enhance the performance of 'sbw', users are encouraged to install other solvers such as 'gurobi' and 'Rmosek', which require special installation. For the installation of gurobi and pogs, please follow the instructions at <https://www.gurobi.com/documentation/current/refman/r_ins_the_r_package.html> and <http://foges.github.io/pogs/stp/r>.

Maintained by Jose R. Zubizarreta. Last updated 8 months ago.

1 stars 1.30 score

cran

CoreMicrobiomeR:Identification of Core Microbiome

The Core Microbiome refers to the group of microorganisms that are consistently present in a particular environment, habitat, or host species. These microorganisms play a crucial role in the functioning and stability of that ecosystem. Identifying these microorganisms can contribute to the emerging field of personalized medicine. The 'CoreMicrobiomeR' is designed to facilitate the identification, statistical testing, and visualization of this group of microorganisms.This package offers three key functions to analyze and visualize microbial community data. This package has been developed based on the research papers published by Pereira et al.(2018) <doi:10.1186/s12864-018-4637-6> and Beule L, Karlovsky P. (2020) <doi:10.7717/peerj.9593>.

Maintained by Mohammad Samir Farooqi. Last updated 12 months ago.

1.00 score

shichaohan

MultiObjMatch:Multi-Objective Matching Algorithm

Matching algorithm based on network-flow structure. Users are able to modify the emphasis on three different optimization goals: two different distance measures and the number of treated units left unmatched. The method is proposed by Pimentel and Kelz (2019) <doi:10.1080/01621459.2020.1720693>. The 'rrelaxiv' package, which provides an alternative solver for the underlying network flow problems, carries an academic license and is not available on CRAN, but may be downloaded from Github at <https://github.com/josherrickson/rrelaxiv/>.

Maintained by Shichao Han. Last updated 9 months ago.

1.00 score 1 scripts

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