Accurate, Adaptable, and Accessible Error Metrics for Predictive Models

Automated Affymetrix Array Analysis Umbrella Package

Automated Affymetrix Array Analysis Base Package

Automated Affymetrix Array Analysis Classification Package

Automated Affymetrix Array Analysis Core Package

Automated Affymetrix Array Analysis Preprocessing Package

Automated Affymetrix Array Analysis Reporting Package

Gene expression enrichment in human brain regions

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

Access to Abbyy Optical Character Recognition (OCR) API

Tools for Approximate Bayesian Computation (ABC)

Data Only: Tools for Approximate Bayesian Computation (ABC)

Computed ABC Analysis

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

ABC Extremes

Implementation of Artificial Bee Colony (ABC) Optimization

Approximate Bayesian Computational Model for Estimating P2

Approximate Bayesian Computation via Random Forests

Tools for ABC Analyses

The Analysis of Biological Data

Load Gap-Free Axon ABF2 Files

Easy Visualization of ABH Genotypes

Combine Multidimensional Arrays

A Biomarker Validation Suit for predicting Survival using gene signature.

Modelling Multivariate Data with Additive Bayesian Networks

Angle-Based Outlier Detection

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

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

Abundant regression and high-dimensional principal fitted components

Abrupt Change-Point or Aberration Detection in Point Series

Functions for Processing and Analyzing Accelerometer Data

Functions for Processing Minute-to-Minute Accelerometer Data

Missing Value Imputation for Accelerometer Data

Creation and Evaluation of Acceptance Sampling Plans

ACC & LMA Graph Plotting

Bayesian Accrual Prediction

Data Quality Visualization Tools for Partially Accruing Data

Categorical data analysis with complete or missing responses

Artificial Components Detection of Differentially Expressed Genes

Tools for Autoregressive Conditional Duration Models

Assay-based Cross-sectional Estimation of incidence rates

Optimal Bayesian Experimental Design using the ACE Algorithm

ace() and avas() for selecting regression transformations

The ACER Method for Extreme Value Estimation

Estimating Dynamic Heritability and Twin Model Comparison

Classes and functions for Array Comparative Genomic Hybridization data.

Robust spline interpolation for dual color array comparative genomic hybridisation data

Analysing Conditional Income Distributions

Align-and-Count Method comparisons of RFLP data

Algorithms for Calculating Microarray Enrichment (ACME)

Implements ACME Estimator of Bird and Bat Mortality by Wind Turbines

Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

Annotated Copy-Number Regions

Modelling dependence with multivariate Archimax (or any user-defined continuous) copulas.

Autoregressive Conditional Poisson

Convenience functions for analytical Customer Relationship Management

A Cost-Minimal Regular Spanning Subgraph with TreeClust

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

Gene Enrichment Analysis from ACSN Maps or GMT Files

Algorithmic Complexity for Short Strings

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

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

Asymptotic Classification Theory for Cognitive Diagnosis

Actigraphy Data Analysis

Animal Activity Statistics

Process activPAL Events Files

Actuarial Functions and Heavy Tailed Distributions

Functions for actuarial scientists

The R Package Ada for Stochastic Boosting

Applies Multiclass AdaBoost.M1, SAMME and Bagging

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

Discrete and Global Optimization Routines

A Class of Adaptive Elastic Net Methods for Censored Data

adapt -- multidimensional numerical integration

Adaptive Mixture Discriminant Analysis

Adaptive Semiparametic Regression

Adaptive Semiparametric Regression with Simultaneous Confidence Bands

Gaussian Mixture Models (GMM)

Adaptive Sparsity Models

Tau-leaping stochastic simulation

Implementation of a generic adaptive Monte Carlo Markov Chain sampler

Adaptive Smoothing of FMRI Data

Adaptive two-stage tests

Binomial and Multinomial Additive Hazards Models

Fit Additive Hazards Models for Survival Analysis

Discover and Install Useful RStudio Addins

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

Additive Regression for Discrete Data

A Package for Analysis of Accelerated Destructive Degradation Test Data

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

'ade4' Tcl/Tk Graphical User Interface

Exploratory Analysis of Genetic and Genomic Data

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

Analysis of Habitat Selection by Animals

Home Range Estimation

Analysis of Animal Movements

Tools to Deal with Raster Maps

adephylo: exploratory analyses for the phylogenetic comparative method.

Adequacy of Probabilistic Models and General Purpose Optimization

Multivariate Multiscale Spatial Analysis

Anderson-Darling GoF test

calculate ad hoc distance thresholds for DNA barcoding identification

Adaptive Smoothing of Digital Images

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

An adaptive lifting scheme algorithm

An Interpretation of the ADM method - automated detection algorithm.

Adaptive Mixture of Student-t distributions

Admixture Graph Manipulation and Fitting

Regularized Model with Selecting the Number of Non-Zeros

Fast Clustering Using Adaptive Density Peak Detection

Spatial point patterns analysis

Annotation-Driven Clustering

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

Wavelet Analysis of Genomic Data from Admixed Populations

Change Point Analysis in ARIMA Forecasting

Download and process AEMO price and demand data

Applied Econometrics with R

Model-Based Estimation of Confounder-Adjusted Attributable Fractions

Analysis of Factorial Experiments

Affymetrix File Parsing SDK

Methods for Affymetrix Oligonucleotide Arrays

Graphics Toolbox for Assessment of Affymetrix Expression Measures

Affymetrix GeneChip software compatibility

structured corruption of affymetrix cel file data

Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Affymetrix Quality Assessment and Analysis Tool

Linear Model of background subtraction and the Langmuir isotherm

Tools for parsing Affymetrix data files

GUI for limma package with Affymetrix microarrays

Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays

Probe Dependent Nearest Neighbours (PDNN) for the affy package

Methods for fitting probe-level models

QC Report Generation for affyBatch objects

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

Easy extraction of individual probes in Affymetrix tiling arrays

Hybrid Simulation and Genome Scan for Dominant Markers

Atomic Force Microscope Image Analysis

Estimation, Diagnostic and Forecasting Functions for ARFIMA models

Run Code in the Background

Accelerated Failure Time Model with Generalized Estimating Equations

Analysis of Growth Data

Agreement of Differential Expression Analysis

Prior distributions for molecular dating

Aggregate Numeric, Date and Categorical Variables by an ID

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

Agilent expression array processing package

Processing and Differential Expression Analysis of Agilent microRNA chips

Aggregation Operators and Preordered Sets

Various Methods for Measuring Agreement

Statistical Tools for Measuring Agreement

Statistical Procedures for Agricultural Research

Agricultural Datasets

Calculate Agreement or Consensus in Ordered Rating Scales

Estimation in Adaptive Group Sequential Trials

Miscellaneous plotting and utility functions

Regularization for semiparametric additive hazards regression

Fast Searching for Multiple Keywords in Multiple Texts

Analytic Hierarchy Process

Estimation and Testing of Average Hazard Ratios

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

Estimation of Box-Cox Power Transformation Parameter

Tools for reading AIDA (http://aida.freehep.org/) files into R

AIM: adaptive index model

Create Pie Like Plot for Completeness

AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype

Associated Kernel Estimations

Interpolation of Irregularly and Regularly Spaced Data

Adaptive Kmeans algorithm based on threshold

Constrained Nonlinear Optimization

Immunoglobulin Clonal Lineage and Diversity Analysis

The Asymmetric Laplace Distribution

Analysis of differential abundance taking sample variation into account

Quantile Regression Using Asymmetric Laplace Distribution

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

Algorithmic Experimental Design

Haplotype Two Snips Out of a Paired Group of Patients

Algebraic statistics in R

Comparison of Alternative Multiple Sequence Alignments

Alignment of Phonetic Sequences Using the 'ALINE' Algorithm

Generate Age-Length Keys for fish populations

Automated Large Linear Analysis Node

Allan Variance Analysis

Allele Imputation and Haplotype Reconstruction from Pedigree Databases

Identifying unique multilocus genotypes where genotyping error and missing data may be present

Allele Retention, Inbreeding, and Demography

A fast, unbiased and exact allelic exact test

Investigates allele specific expression

Computes all of a word's possible spellings.

Alluvial Diagrams

R Client for the Lagotto Altmetrics Platform

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

Obtain Alpha-Outlier Regions for Well-Known Probability Distributions

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

Data to accompany Applied Linear Regression 3rd edition

Data to accompany Applied Linear Regression 4rd edition

Multivariate Curve Resolution Alternating Least Squares (MCR-ALS)

ALS for the Automatic Chemical Exploration of mixtures

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

alternative CDF environments (aka probeset mappings)

Alternative Meta-Analysis Methods

Optimal Experimental Designs for Accelerated Life Testing

Anderson-Moore Algorithm

Another Multidimensional Analysis Package

Compare Gene Expressions from 2-Treatment RNA-Seq Experiments

A Multiple Comparison Perspective

European Commission Annual Macro-Economic (AMECO) Database

Adaptive Management of Epidemiological Interventions

A Program for Missing Data

Additive and Multiplicative Effects Models for Networks and Relational Data

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

Post-processing tool for ADAPT 5

Adaptive Mixed LASSO

A Multidirectional Optimum Ecotope-Based Algorithm

A MORE flexible neural network package

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

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

Analysis of amplicon enrichment panels

Simple and Canonical Correspondence Analysis

3D Anaglyph Plots

Interface to 'Digital Ocean'

Analogue and Weighted Averaging Methods for Palaeoecology

Additional Functions for Use with the Analogue Package

Functions for analysis of fMRI datasets stored in the ANALYZE or NIFTI format.

Analyze (Fuzzy) Time Series

Bidirectional Connector to Anametrix API

Tools for microarray data analysis

Assigning Ancestry Based on Population References

Statistical analysis of surveys with anchoring vignettes

An extended Bayesian Learning Technique developed by Dr. Geoff Webb

Andrews curves

ANES Raking Implementation

Simple Animated Plots For R

Analyze time-coded animal behavior data

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

A Gallery of Animations in Statistics and Utilities to Create Animations

Build Text Prediction Model

Feedforward Artificial Neural Network optimized by Genetic Algorithm

Annotation tools for Affymetrix biological metadata

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

Annotation for microarrays

Annotation Database Interface

Code for Building Annotation Database Packages

Annotation translation functions

Client to access AnnotationHub resources

Transform public data resources into Bioconductor Data Structures

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

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

Analysis of Interactions

Analysis of Means

alpha-NOMINATE Ideal Point Estimator

Anonymize Data Containing Personally Identifiable Information

ANalysis Of Translational Activity (ANOTA).

Version of ant specific to R

Anti-Angiogenic Peptide Prediction

A GUI for Mean Measures of Divergence

Statistical Methods for Anthropometric Data

Implementation of gene expression anti-profiles

Tools for Antitrust Practitioners

programmatic interface to the AntWeb

Analysis of Overdispersed Data

Analysis of Overdispersed Data using S3 methods

Aranda-Ordaz (AO) transformation families

Another Object Orientation System

Adverse Outcome Pathway Analysis

aoristic analysis with spatial output (kml)

Process the Apache Web Server Access Log Files

Generate APA Tables for MS Word

Create American Psychological Association (APA) Style Tables

Age-Period-Cohort Analysis

Affinity Propagation Clustering

Estimate protein complex membership using AP-MS protein data

Analyses of Phylogenetics and Evolution

Phylogenetic Methods for Multiple Gene Data

Another Plot PACKage: stem.leaf, bagplot, faces, spin3R, plotsummary, plothulls, and some slider functions

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

Compute Appell's F1 hypergeometric function

Approximate Path for Penalized Likelihood Estimators

Functions and Data Sets for 'Applied Predictive Modeling'

Amyloid Propensity Prediction Neural Network

Bayesian prediction of complex computer codes

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

Tools for the a Priori Comparison of Regression Modelling Strategies

Amdahl's Profiler, Directed Optimization Made Easy

General Utility Functions for the 'Agricultural Production Systems Simulator'

Analysis the output of Apsim software

Edit, Run and Evaluate APSIM Simulations Easily Using R

apsrtable model-output formatter for social science

Asymmetric Price Transmission

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

Analyses of Phylogenetic Treeshape

Functions to help display air quality model output and monitoring data

Algorithms for Quantitative Pedology

Interface methods to use with an ActiveQuant Master Server

AquaEnv - an integrated development toolbox for aquatic chemical model generation

Segmentation of an autoregressive Gaussian process of order 1

Arabic Stemmer for Text Analysis

A R Adaptive Multiple Importance Sampling

Rigorous Data Reduction and Error Propagation of Ar40 / Ar39 Data

Assessment ratio analysis

Fitting Univariate Censored Linear Regression Model with Autoregressive Errors

Example Datasets from Archaeological Research

Archetypal Analysis

Plant Root System Architecture Analysis Using DART and RSML Files

Tools for Storing, Restoring and Searching for R Objects

Tools for Archiving, Managing and Sharing R Objects via GitHub

Time series autoregressive-based decomposition

Environment air pollution epidemiology: a library for time series analysis

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

Fractional ARIMA (and Other Long Memory) Time Series Modeling

Argos locations filter

Command line optional and positional argument parser.

Command-Line Argument Parser

Improved Communication to Users with Respect to Problems in Function Arguments

Data Analysis Using Regression and Multilevel/Hierarchical Models

"Arnie" box office records 1982-2014

Analysis of Large Affymetrix Microarray Data Sets

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

Copy-Number Analysis of Large Microarray Data Sets

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

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

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

Arps Decline Curve Analysis in R

Application in R for Queueing Analysis and Simulation

Apply a Function to a Margin of an Array

Binarization of numeric data arrays

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

ArrayExpress High Throughput Sequencing Processing Pipeline

Convenience Functions for Arrays

multivariate outlier detection for expression array QA

Assessing array quality on spotted arrays

Quality metrics report for microarray data sets

geneChip Analysis Package

Implementation of wave correction for arrays

Adaptive Robust Regression normalization for Illumina methylation data

Adaptive Rejection Sampling

Aligned Rank Transform for Nonparametric Factorial Analysis

ARTFIMA Model Estimation

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

Aligned Rank Transform

Gene and Pathway p-values computed using the Adaptive Rank Truncated Product

Pathway and Gene-Level Association Test

Mining Association Rules and Frequent Itemsets

Mining NB-Frequent Itemsets and NB-Precise Rules

Mining Frequent Sequences

Visualizing Association Rules and Frequent Itemsets

Interface to the arXiv API

Assign Random Colors to Unique Items in a Vector

Data Sets for "Applied Survival Analysis Using R""

A Collection of Statistical Tools for Biologists

Export R objects to several markup languages

Augmented SCRDA

Simulations for Adaptive Seamless Designs

Reading ASD Binary Files in R

Predict Acetylated Lysine Sites

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

David Scott's ASH Routines

Applied Statistical Hypothesis Tests

'Asio' C++ Header Files

Linkage Map Construction using the MSTmap Algorithm

Animal Social Network Inference and Permutations for Ecologists

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

A General Framework for Multivariate Analysis with Optimal Scaling

Adaptive Sum of Powered Score Test

Augments the Use of 'Asreml' in Fitting Mixed Models

Readable Check Functions to Ensure Code Integrity

A Lightweight Core of the 'assertive' Package

Assertions to Check Properties of Code

Assertions to Check Properties of Data

Assertions to Check Properties of Strings

Assertions to Check Properties of Dates and Times

Assertions to Check Properties of Files

Assertions to Check Properties of Matrices

Assertions to Check Properties of Models

Assertions to Check Properties of Numbers

Assertions to Check Properties of Variables

Assertions for Checking the State of R

Assertions to Check Properties of Sets

Assertions to Check Types of Variables

Assertive Programming for R Analysis Pipelines

Easy pre and post assertions.

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

Optimal pricing of assets with fixed expiry date.

Adaptive Signature Selection and InteGratioN (ASSIGN)

A Suite of R Functions Implementing Spline Smoothing Techniques

Adaptive Subgroup Selection in Group Sequential Trials

Genetic Association Studies

Calculate the Assortativity Coefficient of Weighted and Binary Networks

Statistical Tests for Genetic Association Studies

Aster Models

Astronomy Functions, Tools and Routines

A Computational Tool for Astrochronology

Astronomical Data

Astronomy: time and position functions, misc. utilities

Astronomy Users Library

Applied Statistical Time Series Analysis

Average Shifted Visual Predictive Checks

Asymmetric Linkage Disequilibrium (ALD) for Polymorphic Genetic Data

The Slide-Vector Model for Multidimensional Scaling of Asymmetric Data

Asymptotic statistic

Regression Analysis of Sparse Asynchronous Longitudinal Data

Calculate Power Utilizing Asymptotic Likelihood Ratio Methods

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

Gene Expression Atlas query and gene set enrichment package.

Automatically Tuned Markov Chain Monte Carlo

Advanced Tools for Metrology

Acoustic Traveltime Calculations for 1-D Atmospheric Models

Alternative Time Series Analysis

Evaluation and comparison of expression data and GRNs

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

Population Attributable Risk

Threshold independent performance measures for probabilistic classifiers.

AUC Maximization

Variable Selection with Random Forest and the Area Under the Curve

Audio Interface for R

audiolyzR: Give your data a listen

Bounds for Accounting Populations

Automatic Tracing and Display of Changes to Row Count

Various Methods to Estimate the AUC

Approximate Unconditional and Permutation Tests

Bayesian sampler of the trait-evolutionary process

Sparse Autoencoder for Automatic Learning of Representative Features from Unlabeled Data

Display Multiple Images with Scaled Colors

Automatic interpolation package

Automated Hierarchical Multiple Regression with Assumptions Checking

Partial Least Squares Regression with Backward Selection of Predictors

Minimum Distance Estimation in Autoregressive Model

General-to-Specific (GETS) Modelling

Performs Specification Search in Structural Equation Models

Automated Vector Autoregression Models and Networks

Calculation of Average Population Attributable Fractions and Confidence Intervals

Average Rank Overlap

Adaptive Weights Smoothing

Client for the Amazon Alexa Web Information Services API

Amazon Web Services Request Signatures

R package to use Amazon Web Services

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

A generalization of Fisher's exact test

Interface with Azure Machine Learning Datasets, Experiments and Web Services