Packages — R (Page 1 of 32)
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r 4.0.2
R is a language and environment for statistical computing and graphics. It provides a variety of statistical techniques, such as linear and nonlinear modeling, classical statistical tests, time-series analysis, classification and clustering.…
r-a3 1.0.0
This package supplies tools for tabulating and analyzing the results of predictive models. The methods employed are applicable to virtually any predictive model and make comparisons between different methodologies straightforward. …
r-a4 1.36.0
This package provides a software suite for the automated analysis of Affymetrix arrays. …
r-a4base 1.36.0
This package provides basic features for the automated analysis of Affymetrix arrays. …
r-a4classif 1.36.0
This is the classification package for the automated analysis of Affymetrix arrays. …
r-a4core 1.36.0
This is the core package for the automated analysis of Affymetrix arrays. …
r-a4preproc 1.36.0
This is a package for the automated analysis of Affymetrix arrays. It is used for preprocessing the arrays. …
r-a4reporting 1.36.0
This is a package for the automated analysis of Affymetrix arrays. It provides reporting features. …
r-aasea 1.1.0
Given a protein multiple sequence alignment, it is a daunting task to assess the effects of substitutions along sequence length. The aaSEA package is intended to help researchers to rapidly analyze…
r-abacus 1.0.0
This package provides a set of Shiny apps for effective communication and understanding in statistics. The current version includes properties of normal distribution, properties of sampling distribution, one-sample z and t…
r-abadata 1.12.0
This package provides the data for the gene expression enrichment analysis conducted in the package ABAEnrichment. The package includes three datasets which are derived from the Allen Brain Atlas: 1.…
r-abaenrichment 1.18.0
The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function `aba_enrich' integrates the expression…
r-abbyyr 0.5.5
This package provides tools to get text from images of text using Abbyy Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily OCR images, barcodes, forms, documents with machine…
r-abc 2.1
This package implements several "Approximate Bayesian Computation" (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit. Cross-validation tools are also available for measuring the accuracy of ABC estimates, and to calculate…
r-abc-data 1.0
This package contains data which are used by functions of the abc package which implements several "Approximate Bayesian Computation" (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit. …
r-abc-rap 0.9.0
This package aims to identify candidate genes that are differentially methylated between cases and controls. It applies Student's t-test and delta beta analysis to identify candidate genes containing multiple CpG sites. …
r-abcadm 1.0
This package provides tools to estimate parameters of accumulated damage (load duration) models based on failure time data under a Bayesian framework, using "Approximate Bayesian Computation" (ABC), and to assess long-term reliability under…
r-abcanalysis 1.2.1
Multivariate data sets often differ in several factors or derived statistical parameters, which have to be selected for a valid interpretation. Basing this selection on traditional statistical limits leads occasionally to…
r-abcdefba 0.4
This package provides functions for Constraint Based Simulation using Flux Balance Analysis and informative analysis of the data generated during simulation. …
r-abcoptim 0.15.0
Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as simple as Particle…
r-abcp2 1.2
This package tests the goodness of fit of a distribution of offspring to the Normal, Poisson, and Gamma distribution and estimates the proportional paternity of the second male (P2) based on the…
r-abcrf 1.8.1
This package performs approximate bayesian computation (ABC) model choice and parameter inference via random forests. This machine learning tool named random forests (RF) can conduct selection among the highly complex models…
r-abcrlda 1.0.3
This package offers methods to perform "asymptotically bias-corrected regularized linear discriminant analysis" (ABC_RLDA) for cost-sensitive binary classification. The bias-correction is an estimate of the bias term added to regularized discriminant analysis that…
r-abctools 1.1.3
This `r-abctools' package provides tools for approximate Bayesian computation including summary statistic selection and assessing coverage. This includes recent dimension reduction algorithms to tune the choice of summary statistics, and coverage methods…
r-abd 0.2-8
The `r-abd' package contains data sets and sample code for the Analysis of biological data by Michael Whitlock and Dolph Schluter. …
r-abe 3.0.1
This package performs augmented backward elimination and checks the stability of the obtained model. Augmented backward elimination combines significance or information based criteria with the change in estimate to either select…
r-abemus 1.0.1
This package provides an implementation of "Adaptive Base Error Model in Ultra-deep Sequencing data" (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic "single nucleotide variants" (SNVs)…
r-abf2 0.7-1
This package loads electrophysiology data from ABF2 files, as created by Axon Instruments/Molecular Devices software. Only files recorded in gap-free mode are currently supported. …
r-abhgenotyper 1.0.1
The `r-abhgenotyper' package provides simple imputation, error-correction and plotting capacities for genotype data. The package is supposed to serve as an intermediate but independent analysis tool between the TASSEL GBS pipeline…
r-abind 1.4-5
This package provides tools to combine multidimensional arrays into a single array. This is a generalization of `cbind' and `rbind'. It works with vectors, matrices, and higher-dimensional arrays. It…
r-abjutils 0.2.3
This package implements general purpose tools, such as functions for sampling and basic manipulation of Brazilian lawsuits identification number. It also implements functions for text cleaning, such as accentuation removal. …
r-abn 2.2.2
Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model…
r-abnormality 0.1.0
This package contains functions to implement the methodology and considerations laid out by Marks et al. in the article "Measuring abnormality in high dimensional spaces: applications in biomechanical gait analysis". …
r-abodoutlier 0.1
This package performs angle-based outlier detection on a given data frame. It offers three methods to process data: 1. full but slow implementation using all the data that has…
r-abps 0.3
This package offers an implementation of the "Abnormal blood profile score" (ABPS). The ABPS is a part of the Athlete biological passport program of the World anti-doping agency, which combines several…
r-abseqr 1.6.0
AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. AbseqR empowers the users of abseqPy with plotting and…
r-absfiltergsea 1.5.1
This package provides a function that performs gene-permuting of a gene-set enrichment analysis (GSEA) calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA. …
r-absim 0.2.6
This package provides simulation methods for the evolution of antibody repertoires. The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion.…
r-abstractr 0.1.0
This package provides an R Shiny application to create visual abstracts for original research. A variety of user defined options and formatting are included. …
r-abtest 0.2.1
This package provides functions for Bayesian A/B testing including prior elicitation options based on Kass and Vaidyanathan (1992) `doi:10.1111/j.2517-6161.1992.tb01868.x'. …
r-abundant 1.1
This package provides tools to fit and predict with the high-dimensional principal fitted components model. This model is described by Cook, Forzani, and Rothman (2012) `doi:10.1214/11-AOS962'. …
r-ac3net 1.2.2
This package infers directional Conservative causal core (gene) networks (C3NET). This is a version of the algorithm C3NET with directional network. …
r-aca 1.1
This package offers an interactive function for the detection of breakpoints in series. …
r-acc 1.3.3
This package processes accelerometer data from uni-axial and tri-axial devices and generates data summaries. Also, includes functions to plot, analyze, and simulate accelerometer data. …
r-accelerometry 3.1.2
This package provides a collection of functions that perform operations on time-series accelerometer data, such as identify the non-wear time, flag minutes that are part of an activity bout, and find the…
r-accelmissing 1.4
This package provides a statistical method to impute the missing values in accelerometer data. The methodology includes both parametric and semi-parametric multiple imputations under the zero-inflated Poisson lognormal model. It also…
r-accept 0.7.1
This package allows clinicians to predict the rate and severity of future acute exacerbation in "Chronic Obstructive Pulmonary Disease" (COPD) patients, based on the clinical prediction model published in Adibi et al.…
r-acceptancesampling 1.0-6
This `r-acceptancesampling' provides functionality for creating and evaluating acceptance sampling plans. Acceptance sampling is a methodology commonly used in quality control and improvement. International standards of acceptance sampling provide sampling plans…
r-acclma 1.0
This package contains a function that imports data from a CSV (Comma-Separated Values) file, or uses manually entered data from the format (x, y, weight) and plots the appropriate ACC (Absolute Concentration…
r-accrual 1.3
Subject recruitment for medical research is challenging. Slow patient accrual leads to delay in research. Accrual monitoring during the process of recruitment is critical. Researchers need reliable tools to…
r-accrued 1.4.1
This is a package for visualizing data quality of partially accruing data. …
r-accsda 1.0.0
This package provides an implementation of sparse linear discriminant analysis, which is a supervised classification method for multiple classes. Various novel optimization approaches to this problem are implemented including "alternating direction method…
r-acd 1.5.3
This package provides tools for categorical data analysis with complete or missing responses. …
r-acdm 1.0.4
ACDm is a package for Autoregressive Conditional Duration (ACD, Engle and Russell, 1998) models. It creates trade, price or volume durations from transactions (tic) data, performs diurnal adjustments, fits various ACD…
r-ace2fastq 0.6.0
The ACE file format is used in genomics to store contigs from sequencing machines. This tools converts it into FASTQ format. Both formats contain the sequence characters and their corresponding…
r-acebayes 1.9
Finding an optimal Bayesian experimental design involves maximizing an objective function given by the expectation of some appropriately chosen utility function with respect to the joint distribution of unknown quantities (including responses). …
r-acepack 1.4.1
This package provides ACE and AVAS methods for choosing regression transformations. …
r-acet 1.8.0
This package supports twin models that are able to estimate the dynamic behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines. …
r-acfmperiod 1.0.0
This package support non-robust and robust computations of the sample autocovariance (ACOVF) and sample autocorrelation functions (ACF) of univariate and multivariate processes. The methodology consists in reversing the diagonalization procedure involving the…
r-acid 1.1
This package provides functions for the analysis of income distributions for subgroups of the population as defined by a set of variables like age, gender, region, etc. This entails a Kolmogorov-Smirnov…
r-acm4r 1.0
This is a package to compare sequence fragment lengths or molecular weights from pairs of lanes. The number of matching bands in the "Restriction Fragment Length Polymorphism" (RFLP) data is calculated…
r-acmeeqtl 1.6
This package provides a non-linear model, termed ACME, that reflects a parsimonious biological model for allelic contributions of cis-acting eQTLs. With non-linear least-squares algorithm the maximum likelihood parameters can be estimated. The…
r-acmer 1.1.0
This package provides an implementation of the ACME estimator, described in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran Mortality at Wind Turbines. Unlike most other models, this…
r-acnr 1.0.0
This package provides SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data…
r-acopula 0.9.3
Archimax copulas are a mixture of Archimedean and EV copulas. This package provides definitions of several parametric families of generator and dependence function, computes CDF and PDF, estimates parameters, tests for…
r-acousticndlcoder 1.0.2
Make acoustic cues to use with the R package `ndl'. The package implements functions used in the PLoS ONE paper "Words from spontaneous conversational speech can be recognized with human-like accuracy…
r-acp 2.1
This package supports the analysis of count data exhibiting autoregressive properties, using the "Autoregressive Conditional Poisson" model (ACP(p,q)) proposed by Heinen (2003). …
r-acrm 0.1.1
This package provides convenience functions for data preparation and modeling often used in "analytical customer relationship management" (aCRM). …
r-acrosstic 1.0-3
This is a package for constructing minimum-cost regular spanning subgraph as part of a non-parametric two-sample test for equality of distribution. …
r-acrt 1.0.1
This package provides functions for testing affine hypotheses on the regression coefficient vector in regression models with autocorrelated errors. …
r-acs 2.1.4
This package provides a general toolkit for downloading, managing, analyzing, and presenting data from the U.S. Census (https://www.census.gov/data/developers/data-sets.html), including SF1 (Decennial short-form), SF3 (Decennial long-form), and the American Community Survey (ACS). Confidence…
r-acsnminer 0.16.8.25
This package provides tools to compute and represent gene set enrichment or depletion from your data based on pre-saved maps from the "Atlas of Cancer Signalling Networks" (ACSN) or user imported maps.…
r-acss 0.2-5
The main purpose of this package is to provide the algorithmic complexity for short strings, an approximation of the Kolmogorov Complexity of a short string using the coding theorem method. While…
r-acss-data 1.0
This is a data only package providing the algorithmic complexity of short strings, computed using the coding theorem method. For a given set of symbols in a string, all possible or…
r-acswr 1.0
This is a companion package for the book "A Course in Statistics with R" (ISBN 978-1-119-15272-9.) …
r-actcd 1.2-0
This is a package supporting cluster analysis for cognitive diagnosis based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; `doi:10.1007/s11336-009-9125-0'). Given the sample statistic of sum-scores, cluster analysis techniques can…
r-actfrag 0.1.1
This package provides functions to extract commonly used fragmentation metrics to quantify time accumulation strategies based on minute level actigraphy-measured activity counts data. …
r-actigraphy 1.4.0
This package provides tools for functional linear modeling and analysis of actigraphy data. …
r-activedriver 1.0.0
This package provides a mutation analysis tool that discovers cancer driver genes with frequent mutations in protein signalling sites such as post-translational modifications (phosphorylation, ubiquitination, etc). The Poisson generalized linear regression model…
r-activedriverwgs 1.0.1
This package provides a method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. ActiveDriverWGS detects coding and noncoding driver elements…
r-activepathways 1.0.2
This package represents an integrative method of analyzing multi omics data that conducts enrichment analysis of annotated gene sets. ActivePathways uses a statistical data fusion approach, rationalizes contributing evidence and highlights associated…
r-activity 1.3
This package provides functions to fit kernel density functions to animal activity time data; plot activity distributions; quantify overall levels of activity; statistically compare activity metrics through bootstrapping; and evaluate variation in linear…
r-activitycounts 0.1.2
ActiLife generates activity counts from data collected by Actigraph accelerometers. Actigraph is one of the most common research-grade accelerometers. There is considerable research validating and developing algorithms for human activity using…
r-activityindex 0.3.6
This is a package to read raw accelerometry from GT3X+ accelerometry data and plain table data to calculate the Activity Index from Bai et al. (2016) `doi:10.1371/journal.pone.0160644'. …
r-activpal 0.1.3
This package contains functions to generate pre-defined summary statistics from activPAL events files. The package also contains functions to produce informative graphics that visualize physical activity behaviour and trends. This includes…
r-activpalprocessing 1.0.2
This package performs estimation of physical activity and sedentary behavior variables from activPAL events files. …
r-actogrammr 0.2.3
Read in activity measurements from standard file formats used by circadian rhythm researchers, currently only ClockLab format, and process and plot the data. The central type of plot is the actogram,…
r-actuar 3.0-0
This package provides functions and data sets for actuarial science: modeling of loss distributions; risk theory and ruin theory; simulation of compound models, discrete mixtures and compound hierarchical models; credibility theory. …
r-acuityview 0.1
This package provides a simple method for representing a visual scene as it may be seen by an animal with less acute vision. …
r-ada 2.0-5
This package provides a straightforward, well-documented, and broad boosting routine for classification, ideally suited for small to moderate-sized data sets. It performs discrete, real, and gentle boost under both exponential and logistic…
r-adabag 4.2
This package implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging algorithm using classification trees as individual classifiers. Once these classifiers have been trained, they can be used to predict on new…
r-adagio 0.7.1
This package provides methods and algorithms for discrete optimization, e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and Hooke-Jeeves minimization, and some (evolutionary) global optimization functions. …
r-adamethods 1.2.1
This package is a collection of several algorithms to obtain archetypoids with small and large databases and with both classical multivariate data and functional data (univariate and multivariate). Some of these…
r-adapenetclass 1.2
This package provides methods for variable selection for AFT models. …
r-adapr 2.0.0
This package tracks reading and writing within R scripts that are organized into a directed acyclic graph. It contains an interactive Shiny application `adaprApp()'. It uses Git and file hashes…
r-adapsamp 1.1.1
For distributions whose probability density functions are log-concave, the adaptive rejection sampling algorithm can be used to build envelope functions for sampling. For others, the modified adaptive rejection sampling algorithm, the concave-convex…
r-adaptalint 0.2.4
This package provides tools to infer the code style (which style rules are followed and which ones are not) from one package and use it to check another. This makes it easier…
r-adaptivesparsity 1.6
This package implements the Figueiredo machine learning algorithm for adaptive sparsity and the Wong algorithm for adaptively sparse gaussian geometric models. …
r-additivitytests 1.1-4
This package provides an implementation of the Tukey, Mandel, Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests. …
r-ade4 1.7-15
The ade4 package contains data analysis functions to analyze ecological and environmental data in the framework of Euclidean exploratory methods. …