Renjin.org | Packages

A3

Accurate, Adaptable, and Accessible Error Metrics for Predictive Models

a4

Automated Affymetrix Array Analysis Umbrella Package

a4Base

Automated Affymetrix Array Analysis Base Package

a4Classif

Automated Affymetrix Array Analysis Classification Package

a4Core

Automated Affymetrix Array Analysis Core Package

a4Preproc

Automated Affymetrix Array Analysis Preprocessing Package

a4Reporting

Automated Affymetrix Array Analysis Reporting Package

ABAData

Averaged gene expression in human brain regions from Allen Brain Atlas

ABAEnrichment

Gene expression enrichment in human brain regions

ABarray

Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.

abbyyR

Access to Abbyy Optical Character Recognition (OCR) API

abc

Tools for Approximate Bayesian Computation (ABC)

abc.data

Data Only: Tools for Approximate Bayesian Computation (ABC)

ABC.RAP

Array Based CpG Region Analysis Pipeline

ABCanalysis

Computed ABC Analysis

abcdeFBA

ABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package.

ABCExtremes

ABC Extremes

ABCoptim

Implementation of Artificial Bee Colony (ABC) Optimization

ABCp2

Approximate Bayesian Computational Model for Estimating P2

abcrf

Approximate Bayesian Computation via Random Forests

abctools

Tools for ABC Analyses

abd

The Analysis of Biological Data

abe

Augmented Backward Elimination

abf2

Load Gap-Free Axon ABF2 Files

ABHgenotypeR

Easy Visualization of ABH Genotypes

abind

Combine Multidimensional Arrays

aBioMarVsuit

A Biomarker Validation Suit for predicting Survival using gene signature.

abjutils

Useful Tools for Jurimetrical Analysis Used by the Brazilian Jurimetrics Association

abn

Modelling Multivariate Data with Additive Bayesian Networks

abnormality

Measure a Subject's Abnormality with Respect to a Reference Population

abodOutlier

Angle-Based Outlier Detection

ABPS

The Abnormal Blood Profile Score to Detect Blood Doping

AbsFilterGSEA

Improved False Positive Control of Gene-Permuting GSEA with Absolute Filtering

AbSim

Time Resolved Simulations of Antibody Repertoires

ABSSeq

ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences

abstractr

An R-Shiny Application for Creating Visual Abstracts

abtest

Bayesian A/B Testing

abundant

High-Dimensional Principal Fitted Components and Abundant Regression

Ac3net

Inferring Directional Conservative Causal Core Gene Networks

ACA

Abrupt Change-Point or Aberration Detection in Point Series

acc

Exploring Accelerometer Data

accelerometry

Functions for Processing Accelerometer Data

accelmissing

Missing Value Imputation for Accelerometer Data

AcceptanceSampling

Creation and Evaluation of Acceptance Sampling Plans

ACCLMA

ACC & LMA Graph Plotting

accrual

Bayesian Accrual Prediction

accrued

Data Quality Visualization Tools for Partially Accruing Data

accSDA

Accelerated Sparse Discriminant Analysis

ACD

Categorical data analysis with complete or missing responses

acde

Artificial Components Detection of Differentially Expressed Genes

ACDm

Tools for Autoregressive Conditional Duration Models

Ace

Assay-based Cross-sectional Estimation of incidence rates

ace2fastq

ACE File to FASTQ Converter

acebayes

Optimal Bayesian Experimental Design using the ACE Algorithm

acepack

ACE and AVAS for Selecting Multiple Regression Transformations

acer

The ACER Method for Extreme Value Estimation

ACEt

Estimating Dynamic Heritability and Twin Model Comparison

aCGH

Classes and functions for Array Comparative Genomic Hybridization data.

aCGH.Spline

Robust spline interpolation for dual color array comparative genomic hybridisation data

acid

Analysing Conditional Income Distributions

acm4r

Align-and-Count Method comparisons of RFLP data

ACME

Algorithms for Calculating Microarray Enrichment (ACME)

ACMEeqtl

Estimation of Interpretable eQTL Effect Sizes Using a Log of Linear Model

acmeR

Implements ACME Estimator of Bird and Bat Mortality by Wind Turbines

ACNE

Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

acnr

Annotated Copy-Number Regions

acopula

Modelling Dependence with Multivariate Archimax (or any User-Defined Continuous) Copulas

AcousticNDLCodeR

Coding Sound Files for Use with NDL

acp

Autoregressive Conditional Poisson

aCRM

Convenience functions for analytical Customer Relationship Management

AcrossTic

A Cost-Minimal Regular Spanning Subgraph with TreeClust

acrt

Autocorrelation Robust Testing

acs

Download, Manipulate, and Present American Community Survey and Decennial Data from the US Census

ACSNMineR

Gene Enrichment Analysis from ACSN Maps or GMT Files

acss

Algorithmic Complexity for Short Strings

acss.data

Data Only: Algorithmic Complexity of Short Strings (Computed via Coding Theorem Method)

ACSWR

A Companion Package for the Book "A Course in Statistics with R"

ACTCD

Asymptotic Classification Theory for Cognitive Diagnosis

ActFrag

Activity Fragmentation Metrics Extracted from Minute Level Activity Data

Actigraphy

Actigraphy Data Analysis

ActisoftR

A Toolbox for Parsing Scored Actigraphy Data

ActiveDriver

Finding Cancer Driver Proteins with Enriched Mutations in Post-Translational Modification Sites

ActiveDriverWGS

A Driver Discovery Tool for Cancer Whole Genomes

ActivePathways

Multivariate Pathway Enrichment Analysis

activity

Animal Activity Statistics

ActivityIndex

Activity Index Calculation using Raw Accelerometry Data

activpalProcessing

Process activPAL Events Files

actogrammr

Read in Activity Data and Plot Actograms

actuar

Actuarial Functions and Heavy Tailed Distributions

ActuDistns

Functions for actuarial scientists

AcuityView

A Package for Displaying Visual Scenes as They May Appear to an Animal with Lower Acuity

ada

The R Package Ada for Stochastic Boosting

adabag

Applies Multiclass AdaBoost.M1, SAMME and Bagging

ADaCGH2

Analysis of big data from aCGH experiments using parallel computing and ff objects

adagio

Discrete and Global Optimization Routines

adamethods

Archetypoid Algorithms and Anomaly Detection

AdapEnetClass

A Class of Adaptive Elastic Net Methods for Censored Data

adapr

Implementation of an Accountable Data Analysis Process

AdapSamp

Adaptive Sampling Algorithms

adapt

adapt -- multidimensional numerical integration

adaptalint

Check Code Style Painlessly

adaptDA

Adaptive Mixture Discriminant Analysis

adaptest

Data-Adaptive Statistics for High-Dimensional Multiple Testing

AdaptFit

Adaptive Semiparametic Regression

AdaptFitOS

Adaptive Semiparametric Additive Regression with Simultaneous Confidence Bands and Specification Tests

AdaptGauss

Gaussian Mixture Models (GMM)

adaptiveGPCA

Adaptive Generalized PCA

AdaptiveSparsity

Adaptive Sparsity Models

adaptivetau

Tau-Leaping Stochastic Simulation

adaptMCMC

Implementation of a Generic Adaptive Monte Carlo Markov Chain Sampler

adaptMT

Adaptive P-Value Thresholding for Multiple Hypothesis Testing with Side Information

ADAPTS

Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells

adaptsmoFMRI

Adaptive Smoothing of FMRI Data

adaptTest

Adaptive two-stage tests

AdaSampling

Adaptive Sampling for Positive Unlabeled and Label Noise Learning

ADCT

Adaptive Design in Clinical Trials

addhaz

Binomial and Multinomial Additive Hazard Models

addhazard

Fit Additive Hazards Models for Survival Analysis

addinslist

Discover and Install Useful RStudio Addins

additiveDEA

Additive Data Envelopment Analysis Models

additivityTests

Additivity Tests in the Two Way Anova with Single Sub-class Numbers

addreg

Additive Regression for Discrete Data

ADDT

Analysis of Accelerated Destructive Degradation Test Data

ade4

Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

ade4TkGUI

'ade4' Tcl/Tk Graphical User Interface

adeba

Adaptive Density Estimation by Bayesian Averaging

adegenet

Exploratory Analysis of Genetic and Genomic Data

adegraphics

An S4 Lattice-Based Package for the Representation of Multivariate Data

adehabitat

Analysis of Habitat Selection by Animals

adehabitatHR

Home Range Estimation

adehabitatHS

Analysis of Habitat Selection by Animals

adehabitatLT

Analysis of Animal Movements

adehabitatMA

Tools to Deal with Raster Maps

adephylo

Exploratory Analyses for the Phylogenetic Comparative Method

adepro

A 'shiny' Application for the (Audio-)Visualization of Adverse Event Profiles

adept

Adaptive Empirical Pattern Transformation

adeptdata

Accelerometry Data Sets

AdequacyModel

Adequacy of Probabilistic Models and General Purpose Optimization

adespatial

Multivariate Multiscale Spatial Analysis

adfExplorer

Import from and Export to Amiga Disk Files

ADGofTest

Anderson-Darling GoF test

AdhereR

Adherence to Medications

adhoc

Calculate Ad Hoc Distance Thresholds for DNA Barcoding Identification

adimpro

Adaptive Smoothing of Digital Images

adiv

Analysis of Diversity

AdjBQR

Adjusted Bayesian Quantile Regression Inference

adjclust

Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix

adjustedcranlogs

Remove Automated and Repeated Downloads from 'RStudio' 'CRAN' Download Logs

adk

Anderson-Darling K-Sample Test and Combinations of Such Tests

adklakedata

Adirondack Long-Term Lake Data

adlift

An Adaptive Lifting Scheme Algorithm

ADM3

An Interpretation of the ADM method - automated detection algorithm.

adme16cod.db

Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod)

admisc

Adrian Dusa's Miscellaneous

AdMit

Adaptive Mixture of Student-t Distributions

admixturegraph

Admixture Graph Manipulation and Fitting

ADMM

Algorithms using Alternating Direction Method of Multipliers

ADMMnet

Regularized Model with Selecting the Number of Non-Zeros

ADMMsigma

Penalized Precision Matrix Estimation via ADMM

adnuts

No-U-Turn MCMC Sampling for 'ADMB' and 'TMB' Models

adoption

Modelling Adoption Process in Marketing

adoptr

Adaptive Optimal Two-Stage Designs in R

ADPclust

Fast Clustering Using Adaptive Density Peak Detection

ADPF

Use Least Squares Polynomial Regression and Statistical Testing to Improve Savitzky-Golay

adpss

Design and Analysis of Locally or Globally Efficient Adaptive Designs

ads

Spatial Point Patterns Analysis

adSplit

Annotation-Driven Clustering

AdvBinomApps

Upper Clopper-Pearson Confidence Limits for Burn-in Studies under Additional Available Information

advclust

Object Oriented Advanced Clustering

AdvDif4

Solving 1D Advection Bi-Flux Diffusion Equation

adwave

Wavelet Analysis of Genomic Data from Admixed Populations

adwordsR

Access the 'Google Adwords' API

AEDForecasting

Change Point Analysis in ARIMA Forecasting

aemo

Download and Process AEMO Price and Demand Data

AER

Applied Econometrics with R

AeRobiology

A Computational Tool for Aerobiological Data

AF

Model-Based Estimation of Confounder-Adjusted Attributable Fractions

afc

Generalized Discrimination Score

afCEC

Active Function Cross-Entropy Clustering

afex

Analysis of Factorial Experiments

affluenceIndex

Affluence Indices

affxparser

Affymetrix File Parsing SDK

affy

Methods for Affymetrix Oligonucleotide Arrays

affycomp

Graphics Toolbox for Assessment of Affymetrix Expression Measures

AffyCompatible

Affymetrix GeneChip software compatibility

affycompData

affycomp data

affyContam

structured corruption of affymetrix cel file data

affycoretools

Functions useful for those doing repetitive analyses with Affymetrix GeneChips

affydata

Affymetrix Data for Demonstration Purpose

AffyExpress

Affymetrix Quality Assessment and Analysis Tool

Affyhgu133A2Expr

Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package

Affyhgu133aExpr

Affymetrix Human hgu133a Array (GPL96) Expression Data Package

Affyhgu133Plus2Expr

Affyhgu133Plus2Expr (GPL570) Expression Data Package

affyILM

Linear Model of background subtraction and the Langmuir isotherm

affyio

Tools for parsing Affymetrix data files

affylmGUI

GUI for limma Package with Affymetrix Microarrays

AffymetrixDataTestFiles

Affymetrix data files (CEL, CDF, CHP, EXP, PGF, PSI) for testing

Affymoe4302Expr

Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package

affyPara

Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays

affypdnn

Probe Dependent Nearest Neighbours (PDNN) for the affy package

affyPLM

Methods for fitting probe-level models

affyQCReport

QC Report Generation for affyBatch objects

AffyRNADegradation

Analyze and correct probe positional bias in microarray data due to RNA degradation

AffyTiling

Easy extraction of individual probes in Affymetrix tiling arrays

AFheritability

The Attributable Fraction (AF) Described as a Function of Disease Heritability, Prevalence and Intervention Specific Factors

AFLPsim

Hybrid Simulation and Genome Scan for Dominant Markers

AFM

Atomic Force Microscope Image Analysis

afmToolkit

Functions for Atomic Force Microscope Force-Distance Curves Analysis

afmtools

Estimation, Diagnostic and Forecasting Functions for ARFIMA models

afpt

Tools for Modelling of Animal Flight Performance

after

Run Code in the Background

aftgee

Accelerated Failure Time Model with Generalized Estimating Equations

ag.db

Affymetrix Arabidopsis Genome Array annotation data (chip ag)

agcdf

AGD

Analysis of Growth Data

AGDEX

Agreement of Differential Expression Analysis

aGE

Adaptive Set-Based Gene-Environment Interaction Test for Rare Variants

ageprior

Prior distributions for molecular dating

AggregateR

Aggregate Numeric, Date and Categorical Variables by an ID

aggregation

p-Value Aggregation Methods

aggrisk

Estimate individual level risk using individual case data and spatially aggregated control data

AGHmatrix

Relationship Matrices for Diploid and Autopolyploid Species

agilp

Agilent expression array processing package

AgiMicroRna

Processing and Differential Expression Analysis of Agilent microRNA chips

agop

Aggregation Operators and Preordered Sets

agprobe

Probe sequence data for microarrays of type ag

AGread

Read Data Files from ActiGraph Monitors

agRee

Various Methods for Measuring Agreement

Agreement

Statistical Tools for Measuring Agreement

AgreementInterval

Agreement Interval of Two Measurement Methods

agricolae

Statistical Procedures for Agricultural Research

agridat

Agricultural Datasets

agriTutorial

Tutorial Analysis of Some Agricultural Experiments

agriwater

Evapotranspiration and Energy Fluxes Spatial Analysis

agrmt

Calculate Agreement or Consensus in Ordered Rating Scales

AGSDest

Estimation in Adaptive Group Sequential Trials

agsemisc

Miscellaneous plotting and utility functions

ahaz

Regularization for semiparametric additive hazards regression

AHCytoBands

CytoBands for AnnotationHub

AHEnsDbs

EnsDbs for AnnotationHub

AHMbook

Functions and Data for the Book 'Applied Hierarchical Modeling in Ecology'

ahnr

An Implementation of the Artificial Hydrocarbon Networks

AhoCorasickTrie

Fast Searching for Multiple Keywords in Multiple Texts

ahp

Analytic Hierarchy Process

ahpsurvey

Analytic Hierarchy Process for Survey Data

AHR

Estimation and Testing of Average Hazard Ratios

AICcmodavg

Model Selection and Multimodel Inference Based on (Q)AIC(c)

AID

Box-Cox Power Transformation

aidar

Tools for Reading AIDA Files

AIG

Automatic Item Generator

AIM

AIM: adaptive index model

aimPlot

Create Pie Like Plot for Completeness

AIMS

AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype

aire.zmvm

Download Mexico City Pollution, Wind, and Temperature Data

airGR

Suite of GR Hydrological Models for Precipitation-Runoff Modelling

airGRteaching

Teaching Hydrological Modelling with the GR Rainfall-Runoff Models ('Shiny' Interface Included)

airportr

Convenience Tools for Working with Airport Data

airr

AIRR Data Representation Reference Library

aiRthermo

Atmospheric Thermodynamics and Visualization

airway

RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014

ajv

Another JSON Schema Validator

Ake

Associated Kernel Estimations

akima

Interpolation of Irregularly and Regularly Spaced Data

akmeans

Adaptive Kmeans algorithm based on threshold

akmedoids

Anchored Kmedoids for Longitudinal Data Clustering

ALA4R

Atlas of Living Australia (ALA) Data and Resources in R

alabama

Constrained Nonlinear Optimization

alakazam

Immunoglobulin Clonal Lineage and Diversity Analysis

albopictus

Age-Structured Population Dynamics Model

ald

The Asymmetric Laplace Distribution

ALDEx2

Analysis Of Differential Abundance Taking Sample Variation Into Account

ALDqr

Quantile Regression Using Asymmetric Laplace Distribution

ALEPlot

Accumulated Local Effects (ALE) Plots and Partial Dependence (PD) Plots

aLFQ

Estimating Absolute Protein Quantities from Label-Free LC-MS/MS Proteomics Data

alfred

Downloading Time Series from ALFRED Database for Various Vintages

algaeClassify

Determine Phytoplankton Functional Groups Based on Functional Traits

AlgDesign

Algorithmic Experimental Design

AlgebraicHaploPackage

Haplotype Two Snips Out of a Paired Group of Patients

algorithmia

Allows you to Easily Interact with the Algorithmia Platform

algstat

Algebraic statistics in R

alignfigR

Visualizing Multiple Sequence Alignments with 'ggplot2'

AlignStat

Comparison of Alternative Multiple Sequence Alignments

alineR

Alignment of Phonetic Sequences Using the 'ALINE' Algorithm

ALKr

Generate Age-Length Keys for fish populations

ALL

A data package

allan

Automated Large Linear Analysis Node

allanvar

Allan Variance Analysis

alleHap

Allele Imputation and Haplotype Reconstruction from Pedigree Databases

allelematch

Identifying Unique Multilocus Genotypes where Genotyping Error and Missing Data may be Present

AlleleRetain

Allele Retention, Inbreeding, and Demography

allelic

A fast, unbiased and exact allelic exact test

AllelicImbalance

Investigates Allele Specific Expression

ALLMLL

A subset of arrays from a large acute lymphoblastic leukemia (ALL) study

AllPossibleSpellings

Computes all of a word's possible spellings.

alluvial

Alluvial Diagrams

alm

R Client for the Lagotto Altmetrics Platform

alpaca

Fit GLM's with High-Dimensional k-Way Fixed Effects

alphabetr

Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells

alphahull

Generalization of the Convex Hull of a Sample of Points in the Plane

alphaOutlier

Obtain Alpha-Outlier Regions for Well-Known Probability Distributions

AlphaPart

Partition/Decomposition of Additive Genetic Values by Paths of Information

alphashape3d

Implementation of the 3D Alpha-Shape for the Reconstruction of 3D Sets from a Point Cloud

AlphaSimR

Breeding Program Simulations

alphastable

Inference for Stable Distribution

AlphaVantageClient

Wrapper for Alpha Vantage API

alphavantager

Lightweight R Interface to the Alpha Vantage API

alpine

alpineData

Data for the alpine package vignette

alR

Arc Lengths of Statistical Functions

alr3

Data to Accompany Applied Linear Regression 3rd Edition

alr4

Data to Accompany Applied Linear Regression 4th Edition

ALS

Multivariate Curve Resolution Alternating Least Squares (MCR-ALS)

alsace

ALS for the Automatic Chemical Exploration of mixtures

ALSCPC

Accelerated line search algorithm for simultaneous orthogonal transformation of several positive definite symmetric matrices to nearly diagonal form.

ALSM

Companion to Applied Linear Statistical Models

altcdfenvs

alternative CDF environments (aka probeset mappings)

alternativeSplicingEvents.hg19

Alternative splicing event annotation for Human (hg19)

alternativeSplicingEvents.hg38

Alternative splicing event annotation for Human (hg38)

alterryx

An 'API' Client for the 'Alteryx' Gallery

altmeta

Alternative Meta-Analysis Methods

ALTopt

Optimal Experimental Designs for Accelerated Life Testing

AMA

Anderson-Moore Algorithm

amap

Another Multidimensional Analysis Package

AMAP.Seq

Compare Gene Expressions from 2-Treatment RNA-Seq Experiments

ambhasGW

Ground Water Modelling

AMCP

A Model Comparison Perspective

AMCTestmakeR

Generate LaTeX Code for Auto-Multiple-Choice (AMC)

ameco

European Commission Annual Macro-Economic (AMECO) Database

amei

Adaptive Management of Epidemiological Interventions

Amelia

A Program for Missing Data

amelie

Anomaly Detection with Normal Probability Functions

amen

Additive and Multiplicative Effects Models for Networks and Relational Data

AmericanCallOpt

This package includes pricing function for selected American call options with underlying assets that generate payouts.

amerika

American Politics-Inspired Color Palette Generator

AmesHousing

The Ames Iowa Housing Data

AMGET

Post-processing tool for ADAPT 5

AMIAS

Alternating Minimization Induced Active Set Algorithms

AmigaFFH

Commodore Amiga File Format Handler

aml

Adaptive Mixed LASSO

ammistability

Additive Main Effects and Multiplicative Interaction Model Stability Parameters

AMModels

Adaptive Management Model Manager

AmmoniaConcentration

Un-Ionized Ammonia Concentration

aMNLFA

Automated Fitting of Moderated Nonlinear Factor Analysis Through the 'Mplus' Program

AMOEBA

A Multidirectional Optimum Ecotope-Based Algorithm

AMORE

A MORE flexible neural network package

AmostraBrasil

Generates Samples or Complete List of Brazilian IBGE (Instituto Brasileiro De Geografia e Estatistica) Census Households, Geocoding it by Google Maps

AMOUNTAIN

Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach

AmpAffyExample

Example of Amplified Data

ampd

An Algorithm for Automatic Peak Detection in Noisy Periodic and Quasi-Periodic Signals

amplican

Automated analysis of CRISPR experiments

AmpliconDuo

Statistical Analysis of Amplicon Data of the Same Sample to Identify Artefacts

ampliQueso

Analysis of amplicon enrichment panels

AMR

Antimicrobial Resistance Analysis

amt

Animal Movement Tools

AmyloGram

Prediction of Amyloid Proteins

AnaCoDa

Analysis of Codon Data under Stationarity using a Bayesian Framework

anacor

Simple and Canonical Correspondence Analysis

anaglyph

3D Anaglyph Plots

analogsea

Interface to 'Digital Ocean'

analogue

Analogue and Weighted Averaging Methods for Palaeoecology

analogueExtra

Additional Functions for Use with the Analogue Package

AnalysisPageServer

A framework for sharing interactive data and plots from R through the web

analysisPipelines

Compose Interoperable Analysis Pipelines & Put Them in Production

analytics

Regression Outlier Detection, Stationary Bootstrap, Testing Weak Stationarity, NA Imputation, and Other Tools for Data Analysis

AnalyzeFMRI

Functions for Analysis of fMRI Datasets Stored in the ANALYZE or NIFTI Format

AnalyzeTS

Analyze Fuzzy Time Series

anametrix

Bidirectional Connector to Anametrix API

anamiR

An integrated analysis package of miRNA and mRNA expression data

anapuce

Tools for Microarray Data Analysis

Anaquin

Statistical analysis of sequins

AncestryMapper

Assigning Ancestry Based on Population References

anchoredDistr

Post-Processing for the Method of Anchored Distributions

anchors

Statistical analysis of surveys with anchoring vignettes

AnDE

An extended Bayesian Learning Technique developed by Dr. Geoff Webb

andrews

Andrews curves

anesrake

ANES Raking Implementation

AneuFinder

Analysis of Copy Number Variation in Single-Cell-Sequencing Data

AneuFinderData

WGSCS Data for Demonstration Purposes

ANF

Affinity Network Fusion for Complex Patient Clustering

AnglerCreelSurveySimulation

Simulate a Bus Route Creel Survey of Anglers

angstroms

Tools for 'ROMS' the Regional Ocean Modeling System

aniDom

Inferring Dominance Hierarchies and Estimating Uncertainty

anim.plots

Simple Animated Plots for R

Animal

Analyze time-coded animal behavior data

animalTrack

Animal track reconstruction for high frequency 2-dimensional (2D) or 3-dimensional (3D) movement data.

animation

A Gallery of Animations in Statistics and Utilities to Create Animations

anipaths

Animation of Observed Trajectories Using Spline-Based Interpolation

ANLP

Build Text Prediction Model

anMC

Compute High Dimensional Orthant Probabilities

ANN

Feedforward Artificial Neural Network optimized by Genetic Algorithm

ANN2

Artificial Neural Networks for Anomaly Detection

annaffy

Annotation tools for Affymetrix biological metadata

annmap

Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

annotate

Annotation for microarrays

AnnotationBustR

Extract Subsequences from GenBank Annotations

AnnotationDbi

Annotation Database Interface

AnnotationFilter

Facilities for Filtering Bioconductor Annotation Resources

AnnotationForge

Code for Building Annotation Database Packages

AnnotationFuncs

Annotation translation functions

AnnotationHub

Client to access AnnotationHub resources

AnnotationHubData

Transform public data resources into Bioconductor Data Structures

annotationTools

Annotate microarrays and perform cross-species gene expression analyses using flat file databases.

annotatr

Annotation of Genomic Regions to Genomic Annotations

AnnotLists

AnnotLists: A tool to annotate multiple lists from a specific annotation file.

annovarR

Integrated Framework to Annotate Genetic Variants

AnnuityRIR

Annuity Random Interest Rates

anocva

A Non-Parametric Statistical Test to Compare Clustering Structures

anoint

Analysis of Interactions

ANOM

Analysis of Means

anomalize

Tidy Anomaly Detection

anomaly

Detecting Anomalies in Data

anomalyDetection

Implementation of Augmented Network Log Anomaly Detection Procedures

anominate

Alpha-NOMINATE Ideal Point Estimator

anonymizer

Anonymize Data Containing Personally Identifiable Information

anopheles.db0

Base Level Annotation databases for anopheles

anota

ANalysis Of Translational Activity (ANOTA).

anota2seq

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

ANOVA.TFNs

One-Way Analysis of Variance Based on Triangular Fuzzy Numbers

ANOVAreplication

Test ANOVA Replications by Means of the Prior Predictive p-Value

ANOVAShiny

Interactive Document for Working with Analysis of Variance

ant

Version of ant specific to R

AntAngioCOOL

Anti-Angiogenic Peptide Prediction

antaresEditObject

Edit an 'Antares' Simulation

antaresProcessing

'Antares' Results Processing

antaresRead

Import, Manipulate and Explore the Results of an 'Antares' Simulation

antaresViz

Antares Visualizations

anthro

Computation of the WHO Child Growth Standards

AnthropMMD

An R-Shiny Application for Smith's Mean Measure of Divergence (MMD)

Anthropometry

Statistical Methods for Anthropometric Data

antiProfiles

Implementation of gene expression anti-profiles

antiProfilesData

Normal colon and cancer preprocessed affy data for antiProfile building.

antitrust

Tools for Antitrust Practitioners

antiword

Extract Text from Microsoft Word Documents

AntWeb

programmatic interface to the AntWeb

anyflights

Download Air Travel Data for Specified Years and Airports

anyLib

Install and Load Any Package from CRAN, Bioconductor or Github

anytime

Anything to 'POSIXct' or 'Date' Converter

aod

Analysis of Overdispersed Data

aods3

Analysis of Overdispersed Data using S3 methods

AOfamilies

Aranda-Ordaz (AO) transformation families

aoos

Another Object Orientation System

aop

Adverse Outcome Pathway Analysis

Aoptbdtvc

A-Optimal Block Designs for Comparing Test Treatments with Controls

aoristic

aoristic analysis with spatial output (kml)

apa

Format Outputs of Statistical Tests According to APA Guidelines

ApacheLogProcessor

Process the Apache Web Server Log Files

apaStyle

Generate APA Tables for MS Word

apaTables

Create American Psychological Association (APA) Style Tables

apaText

Create R Markdown Text for Results in the Style of the American Psychological Association (APA)

apc

Age-Period-Cohort Analysis

APCanalysis

Analysis of Unreplicated Orthogonal Experiments using All Possible Comparisons

apcf

Adapted Pair Correlation Function

apcluster

Affinity Propagation Clustering

apComplex

Estimate protein complex membership using AP-MS protein data

apdesign

An Implementation of the Additive Polynomial Design Matrix

ape

Analyses of Phylogenetics and Evolution

apeglm

Approximate posterior estimation for GLM coefficients

apercu

Quick Look at your Data

apex

Phylogenetic Methods for Multiple Gene Data

APFr

Multiple Testing Approach using Average Power Function (APF) and Bayes FDR Robust Estimation

APfun

Geo-Processing Helper Functions

aphid

Analysis with Profile Hidden Markov Models

aplore3

Datasets from Hosmer, Lemeshow and Sturdivant, "Applied Logistic Regression" (3rd Ed., 2013)

aplpack

Another Plot Package: 'Bagplots', 'Iconplots', 'Summaryplots', Slider Functions and Others

APML0

Augmented and Penalized Minimization Method L0

apmsWAPP

Pre- and Postprocessing for AP-MS data analysis based on spectral counts

apng

Convert Png Files into Animated Png

apollo

Tools for Choice Model Estimation and Application

apparent

Accurate Parentage Analysis in the Absence of Guiding Information

appell

Compute Appell's F1 hypergeometric function

APPEstimation

Adjusted Prediction Model Performance Estimation

apple

Approximate Path for Penalized Likelihood Estimators

AppliedPredictiveModeling

Functions and Data Sets for 'Applied Predictive Modeling'

appnn

Amyloid Propensity Prediction Neural Network

approximator

Bayesian prediction of complex computer codes

approxmatch

Approximately Optimal Fine Balance Matching with Multiple Groups

aprean3

Datasets from Draper and Smith "Applied Regression Analysis" (3rd Ed., 1998)

apricom

Tools for the a Priori Comparison of Regression Modelling Strategies

aprof

Amdahl's Profiler, Directed Optimization Made Easy

APSIM

General Utility Functions for the 'Agricultural Production Systems Simulator'

APSIMBatch

Analysis the output of Apsim software

apsimr

Edit, Run and Evaluate APSIM Simulations Easily Using R

apsrtable

apsrtable model-output formatter for social science

apt

Asymmetric Price Transmission

aptg

Automatic Phylogenetic Tree Generator

APtools

Average Positive Predictive Values (AP) for Binary Outcomes and Censored Event Times

apTreeshape

Analyses of Phylogenetic Treeshape

aqfig

Functions to help display air quality model output and monitoring data

aqp

Algorithms for Quantitative Pedology

aqr

Interface methods to use with an ActiveQuant Master Server

AquaEnv

Integrated Development Toolbox for Aquatic Chemical Model Generation

AR

Another Look at the Acceptance-Rejection Method

ar.matrix

Simulate Auto Regressive Data from Precision Matricies

AR1seg

Segmentation of an autoregressive Gaussian process of order 1

arabicStemR

Arabic Stemmer for Text Analysis

arabidopsis.db0

Base Level Annotation databases for arabidopsis

aracne.networks

ARACNe-inferred gene networks from TCGA tumor datasets

ARAMIS

A R Adaptive Multiple Importance Sampling

ArArRedux

Rigorous Data Reduction and Error Propagation of Ar40 / Ar39 Data

aratio

Assessment ratio analysis

arc

Association Rule Classification

ARCensReg

Fitting Univariate Censored Linear Regression Model with Autoregressive Errors

ArchaeoChron

Bayesian Modeling of Archaeological Chronologies

ArchaeoPhases

Post-Processing of the Markov Chain Simulated by 'ChronoModel', 'Oxcal' or 'BCal'

archdata

Example Datasets from Archaeological Research

archetypal

Finds the Archetypal Analysis of a Data Frame

archetypes

Archetypal Analysis

archiDART

Plant Root System Architecture Analysis Using DART and RSML Files

archivist

Tools for Storing, Restoring and Searching for R Objects

archivist.github

Tools for Archiving, Managing and Sharing R Objects via GitHub

ArCo

Artificial Counterfactual Package

ArDec

Time series autoregressive-based decomposition

areal

Areal Weighted Interpolation

areaplot

Plot Stacked Areas and Confidence Bands as Filled Polygons

arena2r

Plots, Summary Statistics and Tools for Arena Simulation Users

ares

Environment air pollution epidemiology: a library for time series analysis

arf3DS4

Activated Region Fitting, fMRI data analysis (3D).

arfima

Fractional ARIMA (and Other Long Memory) Time Series Modeling

argo

Accurate Estimation of Influenza Epidemics using Google Search Data

argon2

Secure Password Hashing

argonDash

Argon Shiny Dashboard Template

argonR

R Interface to Argon HTML Design

argosfilter

Argos locations filter

argparse

Command Line Optional and Positional Argument Parser

argparser

Command-Line Argument Parser

ArgumentCheck

Improved Communication to Users with Respect to Problems in Function Arguments

ARHT

Adaptable Regularized Hotelling's T^2 Test for High-Dimensional Data

ari

Automated R Instructor

ARIbrain

All-Resolution Inference

aricode

Efficient Computations of Standard Clustering Comparison Measures

arkdb

Archive and Unarchive Databases Using Flat Files

arm

Data Analysis Using Regression and Multilevel/Hierarchical Models

armada

A Statistical Methodology to Select Covariates in High-Dimensional Data under Dependence

armspp

Adaptive Rejection Metropolis Sampling (ARMS) via 'Rcpp'

arnie

"Arnie" box office records 1982-2014

AROC

Covariate-Adjusted Receiver Operating Characteristic Curve Inference

aroma.affymetrix

Analysis of Large Affymetrix Microarray Data Sets

aroma.apd

A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]

aroma.cn

Copy-Number Analysis of Large Microarray Data Sets

aroma.core

Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

aroma.light

Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

Arothron

Geometric Morphometrics Analyses

ARpLMEC

Fitting Autoregressive Censored Linear Mixed-Effects Models

ARPobservation

Tools for Simulating Direct Behavioral Observation Recording Procedures Based on Alternating Renewal Processes

arpr

Advanced R Pipes

aRpsDCA

Arps Decline Curve Analysis in R

arqas

Application in R for Queueing Analysis and Simulation

arrangements

Fast Generators and Iterators for Permutations, Combinations and Partitions

arrApply

Apply a Function to a Margin of an Array

ArrayBin

Binarization of numeric data arrays

ArrayExpress

Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

ArrayExpressHTS

ArrayExpress High Throughput Sequencing Processing Pipeline

arrayhelpers

Convenience Functions for Arrays

arrayMvout

multivariate outlier detection for expression array QA

arrayQuality

Assessing array quality on spotted arrays

arrayQualityMetrics

Quality metrics report for microarray data sets

ArrayTools

geneChip Analysis Package

ArrayTV

Implementation of wave correction for arrays

ARRmData

Example dataset for normalization of Illumina 450k Methylation data

ARRmNormalization

Adaptive Robust Regression normalization for Illumina methylation data

ars

Adaptive Rejection Sampling

arse

Area of Resilience to Stress Event

arsenal

An Arsenal of 'R' Functions for Large-Scale Statistical Summaries

ART

Aligned Rank Transform for Nonparametric Factorial Analysis

artfima

ARTFIMA Model Estimation

ARTIVA

Infer a time-varying DBN network from time series data.

ARTool

Aligned Rank Transform

ARTP

Gene and Pathway p-Values Computed using the Adaptive Rank Truncated Product

ARTP2

Pathway and Gene-Level Association Test

arules

Mining Association Rules and Frequent Itemsets

arulesCBA

Classification Based on Association Rules

arulesNBMiner

Mining NB-Frequent Itemsets and NB-Precise Rules

arulesSequences

Mining Frequent Sequences

arulesViz

Visualizing Association Rules and Frequent Itemsets

aRxiv

Interface to the arXiv API

as.color

Assign Random Colors to Unique Items in a Vector

ASAFE

Ancestry Specific Allele Frequency Estimation

asaur

Data Sets for "Applied Survival Analysis Using R""

asbio

A Collection of Statistical Tools for Biologists

ascii

Export R objects to several markup languages

asciiruler

Render an ASCII Ruler

asciiSetupReader

Reads Fixed-Width ASCII Data Files (.txt or .dat) that Have Accompanying Setup Files (.sps or .sas)

ascrda

Augmented SCRDA

asd

Simulations for Adaptive Seamless Designs

asdreader

Reading ASD Binary Files in R

ASEB

Predict Acetylated Lysine Sites

ASGS.foyer

Interface to the Australian Statistical Geography Standard

ASGSCA

Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models

ash

David Scott's ASH Routines

AshkenazimSonChr21

Annotated variants on the chromosome 21, human genome 19, Ashkenazim Trio son sample

ashr

Methods for Adaptive Shrinkage, using Empirical Bayes

asht

Applied Statistical Hypothesis Tests

ASICS

Automatic Statistical Identification in Complex Spectra

ASICS

Automatic Statistical Identification in Complex Spectra

ASICSdata

Example of 1D NMR spectra data for ASICS package

AsioHeaders

'Asio' C++ Header Files

ASIP

Automated Satellite Image Processing

askpass

Safe Password Entry for R, Git, and SSH

aslib

Interface to the Algorithm Selection Benchmark Library

ASMap

Linkage Map Construction using the MSTmap Algorithm

asnipe

Animal Social Network Inference and Permutations for Ecologists

aspace

A collection of functions for estimating centrographic statistics and computational geometries for spatial point patterns

aSPC

An Adaptive Sum of Powered Correlation Test (aSPC) for Global Association Between Two Random Vectors

aspect

A General Framework for Multivariate Analysis with Optimal Scaling

aspi

Analysis of Symmetry of Parasitic Infections

ASpli

Analysis of alternative splicing using RNA-Seq

aSPU

Adaptive Sum of Powered Score Test

asremlPlus

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

ASSA

Applied Singular Spectrum Analysis (ASSA)

AssayCorrector

Detection and Correction of Spatial Bias in HTS Screens

assertable

Verbose Assertions for Tabular Data (Data.frames and Data.tables)

assertive

Readable Check Functions to Ensure Code Integrity

assertive.base

A Lightweight Core of the 'assertive' Package

assertive.code

Assertions to Check Properties of Code

assertive.data

Assertions to Check Properties of Data

assertive.data.uk

Assertions to Check Properties of Strings

assertive.data.us

Assertions to Check Properties of Strings

assertive.datetimes

Assertions to Check Properties of Dates and Times

assertive.files

Assertions to Check Properties of Files

assertive.matrices

Assertions to Check Properties of Matrices

assertive.models

Assertions to Check Properties of Models

assertive.numbers

Assertions to Check Properties of Numbers

assertive.properties

Assertions to Check Properties of Variables

assertive.reflection

Assertions for Checking the State of R

assertive.sets

Assertions to Check Properties of Sets

assertive.strings

Assertions to Check Properties of Strings

assertive.types

Assertions to Check Types of Variables

assertr

Assertive Programming for R Analysis Pipelines

assertthat

Easy Pre and Post Assertions

ASSET

An R package for subset-based association analysis of heterogeneous traits and subtypes

AssetCorr

Estimating Asset Correlations from Default Data

AssetPricing

Optimal Pricing of Assets with Fixed Expiry Date

ASSIGN

Adaptive Signature Selection and InteGratioN (ASSIGN)

assignPOP

Population Assignment using Genetic, Non-Genetic or Integrated Data in a Machine Learning Framework

assist

A Suite of R Functions Implementing Spline Smoothing Techniques

ASSISTant

Adaptive Subgroup Selection in Group Sequential Trials

AssocAFC

Allele Frequency Comparison

assocInd

Implements New and Existing Association Indices for Constructing Animal Social Networks

ASSOCShiny

Interactive Document for Working with Association Rule Mining Analysis

AssocTests

Genetic Association Studies

assortnet

Calculate the Assortativity Coefficient of Weighted and Binary Networks

AssotesteR

Statistical Tests for Genetic Association Studies

AST

Age-Spatial-Temporal Model

aster

Aster Models

aster2

Aster Models

astro

Astronomy Functions, Tools and Routines

astrochron

A Computational Tool for Astrochronology

astrodatR

Astronomical Data

astroFns

Astronomy: time and position functions, misc. utilities

astrolibR

Astronomy Users Library

astsa

Applied Statistical Time Series Analysis

asus

Adaptive SURE Thresholding Using Side Information

asVPC

Average Shifted Visual Predictive Checks

asymLD

Asymmetric Linkage Disequilibrium (ALD) for Polymorphic Genetic Data

asymmetry

Multidimensional Scaling of Asymmetric Data

asympTest

A Simple R Package for Classical Parametric Statistical Tests and Confidence Intervals in Large Samples

AsynchLong

Regression Analysis of Sparse Asynchronous Longitudinal Data

asypow

Calculate Power Utilizing Asymptotic Likelihood Ratio Methods

atable

Create Tables for Reporting Clinical Trials

ATACseqQC

ATAC-seq Quality Control

AtelieR

A GTK GUI for teaching basic concepts in statistical inference, and doing elementary bayesian tests.

ath1121501.db

Affymetrix Arabidopsis ATH1 Genome Array annotation data (chip ath1121501)

ath1121501cdf

ath1121501probe

Probe sequence data for microarrays of type ath1121501

atlantistools

Process and Visualise Output from Atlantis Models

atlas

Stanford 'ATLAS' Search Engine API

AtlasRDF

Gene Expression Atlas query and gene set enrichment package.

atmcmc

Automatically Tuned Markov Chain Monte Carlo

ATmet

Advanced Tools for Metrology

atmopt

Analysis-of-Marginal-Tail-Means

AtmRay

Acoustic Traveltime Calculations for 1-D Atmospheric Models

ATR

Alternative Tree Representation

aTSA

Alternative Time Series Analysis

atsd

Support Querying Axibase Time-Series Database

attachment

Deal with Dependencies

attempt

Tools for Defensive Programming

attfad

Evaluation and comparison of expression data and GRNs

attract

Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

attrCUSUM

Tools for Attribute VSI CUSUM Control Chart

attribrisk

Population Attributable Risk

atus

American Time Use Survey Data

AUC

Threshold independent performance measures for probabilistic classifiers.

AUCell

AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

aucm

AUC Maximization

AUCRF

Variable Selection with Random Forest and the Area Under the Curve

auctestr

Statistical Testing for AUC Data

audio

Audio Interface for R

audiolyzR

audiolyzR: Give your data a listen

audit

Bounds for Accounting Populations

audited

Automatic Tracing and Display of Changes to Row Count

auditor

Model Audit - Verification, Validation, and Error Analysis

augmentedRCBD

Analysis of Augmented Randomised Complete Block Designs

augSIMEX

Analysis of Data with Mixed Measurement Error and Misclassification in Covariates

auk

eBird Data Extraction and Processing in R

aurelius

Generates PFA Documents from R Code and Optionally Runs Them

AurieLSHGaussian

Creates a Neighbourhood Using Locality Sensitive Hashing for Gaussian Projections

auRoc

Various Methods to Estimate the AUC

AUtests

Approximate Unconditional and Permutation Tests

auteur

Bayesian sampler of the trait-evolutionary process

auth0

Secure Authentication in Shiny with Auth0

auto.pca

Automatic Variable Reduction Using Principal Component Analysis

autoBagging

Learning to Rank Bagging Workflows with Metalearning

autocogs

Automatic Cognostic Summaries

AutoDeskR

An Interface to the 'AutoDesk' 'API' Platform

autoencoder

Sparse Autoencoder for Automatic Learning of Representative Features from Unlabeled Data

autoFRK

Automatic Fixed Rank Kriging

autoimage

Multiple Heat Maps for Projected Coordinates

automagic

Automagically Document and Install Packages Necessary to Run R Code

automap

Automatic interpolation package

automl

Deep Learning with Metaheuristic

AutoModel

Automated Hierarchical Multiple Regression with Assumptions Checking

automultinomial

Models for Spatially Correlated Data

AutoPipe

Automated Transcriptome Classifier Pipeline: Comprehensive Transcriptome Analysis

autoplotly

Automatic Generation of Interactive Visualizations for Statistical Results

Autoplotprotein

Development of Visualization Tools for Protein Sequence

autopls

Partial Least Squares Regression with Backward Selection of Predictors

AutoregressionMDE

Minimum Distance Estimation in Autoregressive Model

AutoSEARCH

General-to-Specific (GETS) Modelling

autoSEM

Performs Specification Search in Structural Equation Models

autoshiny

Automatic Transformation of an 'R' Function into a 'shiny' App

AutoStepwiseGLM

Builds Stepwise GLMs via Train and Test Approach

autothresholdr

An R Port of the 'ImageJ' Plugin 'Auto Threshold'

autovarCore

Automated Vector Autoregression Models and Networks

av

Working with Audio and Video

available

Check if the Title of a Package is Available, Appropriate and Interesting

averisk

Calculation of Average Population Attributable Fractions and Confidence Intervals

avgrankoverlap

Average Rank Overlap

aVirtualTwins

Adaptation of Virtual Twins Method from Jared Foster

aweek

Convert Dates to Arbitrary Week Definitions

AWR

'AWS' Java 'SDK' for R

AWR.Athena

'AWS' Athena 'DBI' Wrapper

AWR.Kinesis

Amazon 'Kinesis' Consumer Application for Stream Processing

AWR.KMS

A Simple Client to the 'AWS' Key Management Service

aws

Adaptive Weights Smoothing

aws.alexa

Client for the Amazon Alexa Web Information Services API

aws.cloudtrail

AWS CloudTrail Client Package

aws.comprehend

'AWS Comprehend' Client Package

aws.ec2metadata

Get EC2 Instance Metadata

aws.iam

AWS IAM Client Package

aws.kms

'AWS Key Management Service' Client Package

aws.lambda

AWS Lambda Client Package

aws.polly

Client for AWS Polly

aws.s3

'AWS S3' Client Package

aws.ses

AWS SES Client Package

aws.signature

Amazon Web Services Request Signatures

aws.sns

AWS SNS Client Package

aws.sqs

AWS SQS Client Package

AWS.tools

R package to use Amazon Web Services

aws.transcribe

Client for 'AWS Transcribe'

aws.translate

Client for 'AWS Translate'

awsjavasdk

Boilerplate R Access to the Amazon Web Services ('AWS') Java SDK

awsMethods

Class and Methods Definitions for Packages 'aws', 'adimpro', 'fmri', 'dwi'

awspack

Amazon Web Services Bundle Package

aylmer

A generalization of Fisher's exact test

AzureAuth

Authentication Services for Azure Active Directory

AzureContainers

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

AzureGraph

Simple Interface to 'Microsoft Graph'

AzureKeyVault

Key and Secret Management in 'Azure'

AzureKusto

Interface to 'Kusto'/'Azure Data Explorer'

AzureML

Interface with Azure Machine Learning Datasets, Experiments and Web Services

AzureRMR

Interface to 'Azure Resource Manager'

AzureStor

Storage Management in 'Azure'

AzureVM

Virtual Machines in 'Azure'