Renjin.org | Packages

R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output

CAISEr

Comparison of Algorithms with Iterative Sample Size Estimation

calACS

Calculations for All Common Subsequences

calcWOI

Calculates the Wavelet-Based Organization Index

calendar

Create, Read, Write, and Work with 'iCalander' Files, Calendars and Scheduling Data

CALIB

Calibration model for estimating absolute expression levels from microarray data

CALIBERrfimpute

Multiple Imputation Using MICE and Random Forest

calibFit

Statistical models and tools for assay calibration

calibrar

Automated Parameter Estimation for Complex (Ecological) Models

calibrate

Calibration of Scatterplot and Biplot Axes

calibrateBinary

Calibration for Computer Experiments with Binary Responses

CalibrateSSB

Weighting and Estimation for Panel Data with Non-Response

calibrator

Bayesian Calibration of Complex Computer Codes

CalibratR

Mapping ML Scores to Calibrated Predictions

CaliCo

Code Calibration in a Bayesian Framework

CALINE3

R interface to Fortran 77 implementation of CALINE3

calmate

Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

CAMAN

Finite Mixture Models and Meta-Analysis Tools - Based on C.A.MAN

CAMERA

Collection of annotation related methods for mass spectrometry data

camtrapR

Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses

cancensus

Canadian Census Data and Geography from the 'CensusMapper' API

canceR

A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC.

cancerclass

Development and validation of diagnostic tests from high-dimensional molecular data

cancerdata

Development and validation of diagnostic tests from high-dimensional molecular data: Datasets

CancerInSilico

An R interface for computational modeling of tumor progression

CancerSubtypes

Cancer subtypes identification, validation and visualization based on multiple genomic data sets

cancerTiming

Estimation of Temporal Ordering of Cancer Abnormalities

CAnD

Perform Chromosomal Ancestry Differences (CAnD) Analyses

candisc

Visualizing Generalized Canonical Discriminant and Canonical Correlation Analysis

canine.db

Affymetrix canine annotation data (chip canine)

canine.db0

Base Level Annotation databases for canine

canine2.db

Affymetrix canine2 annotation data (chip canine2)

canine2probe

Probe sequence data for microarrays of type canine2

canineprobe

Probe sequence data for microarrays of type canine

Canopy

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing

canprot

Chemical Composition of Differential Protein Expression

cansim

Accessing Statistics Canada Data Table and Vectors

CANSIM2R

Directly Extracts Complete CANSIM Data Tables

canvasXpress

Visualization Package for CanvasXpress in R

caOmicsV

Visualization of multi-dimentional cancer genomics data

cap

Covariate Assisted Principal (CAP) Regression for Covariance Matrix Outcomes

cape

Combined Analysis of Pleiotropy and Epistasis

caper

Comparative Analyses of Phylogenetics and Evolution in R

capitalR

Capital Budgeting Analysis, Annuity Loan Calculations and Amortization Schedules

capme

Covariate Adjusted Precision Matrix Estimation

CaPO4Sim

A Virtual Patient Simulator in the Context of Calcium and Phosphate Homeostasis

captioner

Numbers Figures and Creates Simple Captions

capushe

CAlibrating Penalities Using Slope HEuristics

capwire

Estimates population size from non-invasive sampling

caRamel

Automatic Calibration by Evolutionary Multi Objective Algorithm

CARBayes

Spatial Generalised Linear Mixed Models for Areal Unit Data

CARBayesdata

Data Used in the Vignettes Accompanying the CARBayes and CARBayesST Packages

CARBayesST

Spatio-Temporal Generalised Linear Mixed Models for Areal Unit Data

carcass

Estimation of the Number of Fatalities from Carcass Searches

carData

Companion to Applied Regression Data Sets

cardidates

Identification of Cardinal Dates in Ecological Time Series

Cardinal

A mass spectrometry imaging toolbox for statistical analysis

CardinalWorkflows

Datasets and workflows for the Cardinal mass spectrometry imaging package

cardioModel

Cardiovascular Safety Exposure-Response Modeling in Early-Phase Clinical Studies

care

High-Dimensional Regression and CAR Score Variable Selection

CARE1

Statistical package for population size estimation in capture-recapture models.

careless

Procedures for Computing Indices of Careless Responding

carfima

Continuous-Time Fractionally Integrated ARMA Process for Irregularly Spaced Long-Memory Time Series Data

caribou

Estimation of caribou abundance based on large scale aggregations monitored by radio telemetry

CarletonStats

Functions for Statistics Classes at Carleton College

caroline

A Collection of Database, Data Structure, Visualization, and Utility Functions for R

carpenter

Build Common Tables of Summary Statistics for Reports

caRpools

CRISPR AnalyzeR for Pooled CRISPR Screens

CARramps

Reparameterized and marginalized posterior sampling for conditional autoregressive models

CARrampsOcl

Reparameterized and marginalized posterior sampling for conditional autoregressive models, OpenCL implementation

CARRoT

Predicting Categorical and Continuous Outcomes Using One in Ten Rule

CARS

Covariate Assisted Ranking and Screening for Large-Scale Two-Sample Inference

carSurv

Correlation-Adjusted Regression Survival (CARS) Scores

cartools

Tools for Understanding Highway Performance

carx

Censored Autoregressive Model with Exogenous Covariates

Cascade

Selection, Reverse-Engineering and Prediction in Cascade Networks

CascadeData

Experimental Data of Cascade Experiments in Genomics

cascsim

Casualty Actuarial Society Individual Claim Simulator

casebase

Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression

caseMatch

Identify Similar Cases for Qualitative Case Studies

CASMAP

Detection of Statistically Significant Combinations of SNPs in Association Mapping

casper

Characterization of Alternative Splicing based on Paired-End Reads

CAST

'caret' Applications for Spatial-Temporal Models

cat

Analysis of categorical-variable datasets with missing values

catch

Covariate-Adjusted Tensor Classification in High-Dimensions

catchr

Taking the Pain Out of Catching and Handling Conditions

catcont

Test, Identify, Select and Mutate Categorical or Continuous Values

catdap

Categorical Data Analysis Program Package

CatDyn

Fishery Stock Assessment by Catch Dynamics Models

cate

High Dimensional Factor Analysis and Confounder Adjusted Testing and Estimation

categoryCompare

Meta-analysis of high-throughput experiments using feature annotations

cati

Community Assembly by Traits: Individuals and Beyond

catIrt

An R Package for Simulating IRT-Based Computerized Adaptive Tests

CATkit

Chronomics Analysis Toolkit (CAT): Periodicity Analysis

catlearn

Formal Psychological Models of Categorization and Learning

catmap

Case-Control and TDT Meta-Analysis Package

caTools

Tools: moving window statistics, GIF, Base64, ROC AUC, etc.

CatPredi

Optimal Categorisation of Continuous Variables in Prediction Models

catR

Generation of IRT Response Patterns under Computerized Adaptive Testing

catseyes

Create Catseye Plots Illustrating the Normal Distribution of the Means

catspec

Special models for categorical variables

catSurv

Computerized Adaptive Testing for Survey Research

CATTexact

Computation of the p-Value for the Exact Conditional Cochran-Armitage Trend Test

causaldrf

Tools for Estimating Causal Dose Response Functions

causaleffect

Deriving Expressions of Joint Interventional Distributions and Transport Formulas in Causal Models

CausalGAM

Estimation of Causal Effects with Generalized Additive Models

CausalImpact

Inferring Causal Effects using Bayesian Structural Time-Series Models

CausalKinetiX

Learning Stable Structures in Kinetic Systems

causalMGM

Causal Learning of Mixed Graphical Models

causalsens

Selection Bias Approach to Sensitivity Analysis for Causal Effects

causalweight

Estimation Methods for Causal Inference Based on Inverse Probability Weighting

Causata

Analysis utilities for binary classification and Causata users.

CAVIAR

Collection of Functions for Processing, Visualizing and Analyzing Cambial Activity and Wood Formation Monitoring Data

CB2

CRISPR Pooled Screen Analysis using Beta-Binomial Test

cbaf

Multiple automated functions for cbioportal.org

cbar

Contextual Bayesian Anomaly Detection in R

CBCgrps

Compare Baseline Characteristics Between Groups

cbinom

Continuous Analog of a Binomial Distribution

cbird

Clustering of Multivariate Binary Data with Dimension Reduction via L1-Regularized Likelihood Maximization

cbsem

Simulation, Estimation and Segmentation of Composite Based Structural Equation Models

cbsodataR

Statistics Netherlands (CBS) Open Data API Client

CCAGFA

Bayesian Canonical Correlation Analysis and Group Factor Analysis

ccaPP

(Robust) Canonical Correlation Analysis via Projection Pursuit

cccrm

Concordance Correlation Coefficient for Repeated (and Non-Repeated) Measures

ccda

Combined Cluster and Discriminant Analysis

ccdata

Data for Combination Connectivity Mapping (ccmap) Package

ccdrAlgorithm

CCDr Algorithm for Learning Sparse Gaussian Bayesian Networks

ccems

Combinatorially Complex Equilibrium Model Selection

cchs

Cox Model for Case-Cohort Data with Stratified Subcohort-Selection

CCl4

Carbon Tetrachloride (CCl4) treated hepatocytes

cclust

Convex Clustering Methods and Clustering Indexes

CCMnet

Simulate Congruence Class Model for Networks

CCP

Significance Tests for Canonical Correlation Analysis (CCA)

CCpop

One and two locus GWAS of binary phenotype with case-control-population design

CCPROMISE

PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data

ccRemover

Removes the Cell-Cycle Effect from Single-Cell RNA-Sequencing Data

ccrs

Correct and Cluster Response Style Biased Data

cctools

Tools for the Continuous Convolution Trick in Nonparametric Estimation

CCTpack

Consensus Analysis, Model-Based Clustering, and Cultural Consensus Theory Applications

cda

Coupled-Dipole Approximation for Electromagnetic Scattering by Three-Dimensional Clusters of Sub-Wavelength Particles

cdcfluview

Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal

cdcsis

Conditional Distance Correlation Based Feature Screening and Conditional Independence Inference

CDECRetrieve

Retrieve Historical and Near Realtime Data from CDEC

CDF.PSIdekick

Evaluate Differentially Private Algorithms for Publishing Cumulative Distribution Functions

cdfquantreg

Quantile Regression for Random Variables on the Unit Interval

CDFt

Statistical downscaling through CDF-transform

CDLasso

Coordinate Descent Algorithms for Lasso Penalized L1, L2, and Logistic Regression

cdlTools

Tools to Download and Work with USDA Cropscape Data

CDNmoney

Components of Canadian Monetary and Credit Aggregates

cdparcoord

Top Frequency-Based Parallel Coordinates

CDROM

Phylogenetically Classifies Retention Mechanisms of Duplicate Genes from Gene Expression Data

cds

Constrained Dual Scaling for Detecting Response Styles

CDVine

Statistical Inference of C- And D-Vine Copulas

CDVineCopulaConditional

Sampling from Conditional C- and D-Vine Copulas

CEAmarkov

Cost-Effectiveness Analysis using Markov Models

cec2005benchmark

Benchmark for the CEC 2005 Special Session on Real-Parameter Optimization

cec2013

Benchmark functions for the Special Session and Competition on Real-Parameter Single Objective Optimization at CEC-2013

CEGO

Combinatorial Efficient Global Optimization

celegans.db

Affymetrix celegans annotation data (chip celegans)

celegansprobe

Probe sequence data for microarrays of type celegans

celestial

Collection of Common Astronomical Conversion Routines and Functions

cellbaseR

Querying annotation data from the high performance Cellbase web

cellHTS2

Analysis of cell-based screens - revised version of cellHTS

cellity

Quality Control for Single-Cell RNA-seq Data

CellMapper

Predict genes expressed selectively in specific cell types

CellMapperData

Pre-processed data for use with the CellMapper package

CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

cellranger

Translate Spreadsheet Cell Ranges to Rows and Columns

cellscape

Explores single cell copy number profiles in the context of a single cell tree

CellScore

Tool for Evaluation of Cell Identity from Transcription Profiles

cellTree

Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure

cellVolumeDist

Functions to fit cell volume distributions and thereby estimate cell growth rates and division times

CEMiTool

Co-expression Modules identification Tool

CENFA

Climate and Ecological Niche Factor Analysis

censCov

Linear Regression with a Randomly Censored Covariate

CensMixReg

Censored Linear Mixture Regression Models

CensRegMod

Fits Normal and Student-t Censored Regression Model

censusGeography

Changes United States Census Geographic Code into Name of Location

centralplot

Show the Strength of Relationships Between Centre and Peripheral Items

CEoptim

Cross-Entropy R Package for Optimization

CepLDA

Discriminant Analysis of Time Series in the Presence of Within-Group Spectral Variability

cepp

Context Driven Exploratory Projection Pursuit

CerioliOutlierDetection

Outlier Detection Using the Iterated RMCD Method of Cerioli (2010)

CeRNASeek

Identification and Analysis of ceRNA Regulation

cernn

Covariance Estimation Regularized by Nuclear Norm Penalties

ceu1kg

CEU (N=60) genotypes from 1000 genomes pilot phase I

ceu1kgv

expression + genotype on 79 unrelated CEU individuals

ceuhm3

ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort

CexoR

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

CFAssay

Statistical analysis for the Colony Formation Assay

CFC

Cause-Specific Framework for Competing-Risk Analysis

CfEstimateQuantiles

Estimate quantiles using any order Cornish-Fisher expansion

cffdrs

Canadian Forest Fire Danger Rating System

cg

Compare Groups, Analytically and Graphically

cgAUC

Calculate AUC-type measure when gold standard is continuous and the corresponding optimal linear combination of variables with respect to it.

cgdsr

R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)

cgdv17

Complete Genomics Diversity Panel, chr17 on 46 individuals

CGEN

An R package for analysis of case-control studies in genetic epidemiology

cgh

Microarray CGH analysis using the Smith-Waterman algorithm

CGHbase

CGHbase: Base functions and classes for arrayCGH data analysis.

CGHcall

Calling aberrations for array CGH tumor profiles.

cghFLasso

Detecting hot spot on CGH array data with fused lasso regression.

cghMCR

Find chromosome regions showing common gains/losses

CGHnormaliter

Normalization of array CGH data with imbalanced aberrations.

cghRA

Array CGH Data Analysis and Visualization

CGHregions

Dimension Reduction for Array CGH Data with Minimal Information Loss.

cghseg

Segmentation Methods for Array CGH Analysis

cglasso

L1-Penalized Censored Gaussian Graphical Models

cglm

Fits Conditional Generalized Linear Models

cgmanalysis

Clean and Analyze Continuous Glucose Monitor Data

CGManalyzer

Continuous Glucose Monitoring Data Analyzer

CGPfunctions

Powell Miscellaneous Functions for Teaching and Learning Statistics

ChainLadder

Statistical Methods and Models for Claims Reserving in General Insurance

ChAMP

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

chandwich

Chandler-Bate Sandwich Loglikelihood Adjustment

changedetection

Nonparametric Change Detection in Multivariate Linear Relationships

changepoint.mv

Changepoint Analysis for Multivariate Time Series

changepoint.np

Methods for Nonparametric Changepoint Detection

changepointsHD

Change-Point Estimation for Expensive and High-Dimensional Models

changepointsVar

Change-Points Detections for Changes in Variance

ChangepointTesting

Change Point Estimation for Clustered Signals

ChannelAttribution

Markov Model for the Online Multi-Channel Attribution Problem

ChannelAttributionApp

Shiny Web Application for the Multichannel Attribution Problem

CharFun

Numerical Computation Cumulative Distribution Function and Probability Density Function from Characteristic Function

CHARGE

CHARGE: CHromosome Assessment in R from Gene Expression data

ChargeTransport

Charge Transfer Rates and Charge Carrier Mobilities

charlson

Converts listwise icd9 data into comorbidity count and Charlson Index

charm

Analysis of DNA methylation data from CHARM microarrays

charmData

An example dataset for use with the charm package

chartql

Simplified Language for Plots and Charts

checkarg

Check the Basic Validity of a (Function) Argument

checkLuhn

Checks if a Number is Valid Using the Luhn Algorithm

checkpoint

Install Packages from Snapshots on the Checkpoint Server for Reproducibility

checkr

Check the Properties of Common R Objects

cheddar

Analysis and Visualisation of Ecological Communities

cheese

Tools for Intuitive and Flexible Statistical Analysis Workflows

chemCal

Calibration Functions for Analytical Chemistry

ChemmineOB

R interface to a subset of OpenBabel functionalities

chemmodlab

A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models

chemometrics

Multivariate Statistical Analysis in Chemometrics

ChemometricsWithR

Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences

chemosensors

A tool for the design of synthetic experiments in machine olfaction.

ChemoSpec

Exploratory Chemometrics for Spectroscopy

ChemoSpec2D

Exploratory Chemometrics for 2D Spectroscopy

ChemoSpecUtils

Functions Supporting Packages ChemoSpec and ChemoSpec2D

cherry

Multiple Testing Methods for Exploratory Research

cheung2010

resources for genetics of gene expression based on Cheung et al 2010

CHFF

Closest History Flow Field Forecasting for Bivariate Time Series

chi2x3way

Partitioning Chi-Squared and Tau Index for Three-Way Contingency Tables

ChIC

Quality Control Pipeline for ChIP-Seq Data

Chicago

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

chicken.db

Affymetrix chicken annotation data (chip chicken)

chicken.db0

Base Level Annotation databases for chicken

chickenprobe

Probe sequence data for microarrays of type chicken

childsds

Data and Methods Around Reference Values in Pediatrics

ChillModels

Processing Chill and Heat Models for Temperate Fruit Trees

chillR

Statistical Methods for Phenology Analysis in Temperate Fruit Trees

chimera

A package for secondary analysis of fusion products

chimp.db0

Base Level Annotation databases for chimp

chinese.misc

Miscellaneous Tools for Chinese Text Mining and More

ChIPanalyser

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPComp

Quantitative comparison of multiple ChIP-seq datasets

chipenrich

Gene Set Enrichment For ChIP-seq Peak Data

ChIPexoQualExample

Example data for the ChIPexoQual package, which implements a quality control pipeline for ChIP-exo data

chipPCR

Toolkit of Helper Functions to Pre-Process Amplification Data

ChIPpeakAnno

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

ChIPseeker

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

chipseq

chipseq: A package for analyzing chipseq data

ChIPseqR

Identifying Protein Binding Sites in High-Throughput Sequencing Data

ChIPSeqSpike

ChIP-Seq data scaling according to spike-in control

ChIPXpress

ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles

chngpt

Estimation and Hypothesis Testing for Threshold Regression

CHNOSZ

Thermodynamic Calculations and Diagrams for Geochemistry

cholera

Amend, Augment and Aid Analysis of John Snow's Cholera Map

CholWishart

Cholesky Decomposition of the Wishart Distribution

chopsticks

The 'snp.matrix' and 'X.snp.matrix' Classes

choroplethr

Simplify the Creation of Choropleth Maps in R

choroplethrAdmin1

Contains an Administrative-Level-1 Map of the World

choroplethrMaps

Contains Maps Used by the 'choroplethr' Package

chromDraw

chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.

chromoMap

Interactive Visualization and Mapping of Chromosomes

chromoR

Analysis of chromosomal interactions data (correction, segmentation and comparison)

chromPlot

Global visualization tool of genomic data

chromstaR

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

chromstaRData

ChIP-seq data for Demonstration Purposes

chromswitch

An R package to detect chromatin state switches from epigenomic data

chron

Chronological Objects which can Handle Dates and Times

CHRONOS

CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

chunked

Chunkwise Text-File Processing for 'dplyr'

CIDnetworks

Generative Models for Complex Networks with Conditionally Independent Dyadic Structure

CIEE

Estimating and Testing Direct Effects in Directed Acyclic Graphs using Estimating Equations

CIFsmry

Weighted summary of cumulative incidence functions

cifti

Toolbox for Connectivity Informatics Technology Initiative ('CIFTI') Files

cimis

R package for retrieving data from CIMIS.

CINNA

Deciphering Central Informative Nodes in Network Analysis

CINOEDV

Co-Information based N-Order Epistasis Detector and Visualizer

cir

Centered Isotonic Regression and Dose-Response Utilities

CircMLE

Maximum Likelihood Analysis of Circular Data

CircNNTSR

Statistical Analysis of Circular Data using Nonnegative Trigonometric Sums (NNTS) Models

CircOutlier

Detection of Outliers in Circular-Circular Regression

CircSpaceTime

Spatial and Spatio-Temporal Bayesian Model for Circular Data

CircStats

Circular Statistics, from "Topics in Circular Statistics" (2001)

circumplex

Analysis and Visualization of Circular Data

CISE

Common and Individual Structure Explained for Multiple Graphs

cisPath

Visualization and management of the protein-protein interaction networks.

citbcmst

CIT Breast Cancer Molecular SubTypes Prediction

citccmst

CIT Colon Cancer Molecular SubTypes Prediction

Cite

An RStudio Addin to Insert BibTex Citation in Rmarkdown Documents

ciTools

Confidence or Prediction Intervals, Quantiles, and Probabilities for Statistical Models

citr

'RStudio' Add-in to Insert Markdown Citations

citrusprobe

Probe sequence data for microarrays of type citrus

CityPlot

Visualization of structure and contents of a database

CityWaterBalance

Track Flows of Water Through an Urban System

ciuupi

Confidence Intervals Utilizing Uncertain Prior Information

civis

R Client for the 'Civis data science API'

CJAMP

Copula-Based Joint Analysis of Multiple Phenotypes

ckanr

Client for the Comprehensive Knowledge Archive Network ('CKAN') 'API'

CKLRT

Composite Kernel Machine Regression Based on Likelihood Ratio Test

Claddis

Measuring Morphological Diversity and Evolutionary Tempo

cladoRcpp

C++ Implementations of Phylogenetic Cladogenesis Calculations

CLAG

An unsupervised non hierarchical clustering algorithm handling biological data

clam

Classical Age-Depth Modelling of Cores from Deposits

ClamR

Time Series Modeling for Climate Change Proxies

clariomdhumanprobeset.db

Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset)

clariomdhumantranscriptcluster.db

Affymetrix clariomdhuman annotation data (chip clariomdhumantranscriptcluster)

clariomshumanhttranscriptcluster.db

Affymetrix clariomshumanht annotation data (chip clariomshumanhttranscriptcluster)

clariomshumantranscriptcluster.db

Affymetrix clariomshuman annotation data (chip clariomshumantranscriptcluster)

clariomsmousehttranscriptcluster.db

Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster)

clariomsmousetranscriptcluster.db

Affymetrix clariomsmouse annotation data (chip clariomsmousetranscriptcluster)

clariomsrathttranscriptcluster.db

Affymetrix clariomsratht annotation data (chip clariomsrathttranscriptcluster)

clariomsrattranscriptcluster.db

Affymetrix clariomsrat annotation data (chip clariomsrattranscriptcluster)

ClassComparison

Classes and Methods for "Class Comparison" Problems on Microarrays

ClassDiscovery

Classes and Methods for "Class Discovery" with Microarrays or Proteomics

classGraph

Construct Graphs of S4 Class Hierarchies

classifierplots

Generates a Visualization of Classifier Performance as a Grid of Diagnostic Plots

classifly

Explore classification models in high dimensions

classify

Classification Accuracy and Consistency under IRT models.

ClassifyR

A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

classyfire

Robust multivariate classification using highly optimised SVM ensembles

classyfireR

R Interface to the ClassyFire RESTful API

cldr

Language Identifier based on CLD library

cleandata

To Inspect and Manipulate Data; and to Keep Track of This Process

cleanEHR

The Critical Care Clinical Data Processing Tools

cleangeo

Cleaning Geometries from Spatial Objects

cleanNLP

A Tidy Data Model for Natural Language Processing

cleanUpdTSeq

This package classifies putative polyadenylation sites as true or false/internally oligodT primed

clere

Simultaneous Variables Clustering and Regression

clespr

Composite Likelihood Estimation for Spatial Data

cli

Helpers for Developing Command Line Interfaces

ClickClust

Model-Based Clustering of Categorical Sequences

clickR

Fix Data and Create Report Tables from Different Objects

clickstream

Analyzes Clickstreams Based on Markov Chains

clifro

Easily Download and Visualise Climate Data from CliFlo

CliftLRD

Complex-Valued Wavelet Lifting Estimators of the Hurst Exponent for Irregularly Sampled Time Series

clikcorr

Censoring Data and Likelihood-Based Correlation Estimation

clim.pact

Climate analysis and empirical-statistical downscaling (ESD) package for monthly and daily data.

climateStability

Estimating Climate Stability from Climate Model Data

climatol

Climate Tools (Series Homogenization and Derived Products)

climbeR

Calculate Average Minimal Depth of a Maximal Subtree for 'ranger' Package Forests

ClimClass

Climate Classification According to Several Indices

ClimDown

Climate Downscaling Library for Daily Climate Model Output

clime

Constrained L1-minimization for Inverse (covariance) Matrix Estimation

ClimProjDiags

Set of Tools to Compute Various Climate Indices

climtrends

Statistical Methods for Climate Sciences

clinDR

Simulation and Analysis Tools for Clinical Dose Response Modeling

clinfun

Clinical Trial Design and Data Analysis Functions

ClinicalRobustPriors

Robust Bayesian Priors in Clinical Trials: An R Package for Practitioners

ClinicalTrialSummary

Summary Measures for Clinical Trials with Survival Outcomes

ClinReport

Statistical Reporting in Clinical Trials

clippda

A package for the clinical proteomic profiling data analysis

clipper

Gene Set Analysis Exploiting Pathway Topology

clipr

Read and Write from the System Clipboard

cliqueMS

Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

CLLmethylation

Methylation data of primary CLL samples in PACE project

CLME

Constrained Inference for Linear Mixed Effects Models

clogitL1

Fitting Exact Conditional Logistic Regression with Lasso and Elastic Net Penalties

clogitLasso

Sparse Conditional Logistic Regression for Matched Studies

CloneSeeker

Seeking and Finding Clones in Copy Number and Sequencing Data

clonotypeR

High throughput analysis of T cell antigen receptor sequences

clordr

Composite Likelihood Inference and Diagnostics for Replicated Spatial Ordinal Data

cloudml

Interface to the Google Cloud Machine Learning Platform

clr

Curve Linear Regression via Dimension Reduction

clrdag

Constrained Likelihood Ratio Tests for a Directed Acyclic Graph

clst

Classification by local similarity threshold

clstutils

Tools for performing taxonomic assignment.

clttools

Central Limit Theorem Experiments (Theoretical and Simulation)

clubSandwich

Cluster-Robust (Sandwich) Variance Estimators with Small-Sample Corrections

CluMix

Clustering and Visualization of Mixed-Type Data

clusrank

Wilcoxon Rank Sum Test for Clustered Data

clust.bin.pair

Statistical Methods for Analyzing Clustered Matched Pair Data

clustDRM

Clustering Dose-Response Curves and Fitting Appropriate Models to Them

clustEff

Clusters of Effects Curves in Quantile Regression Models

cluster

"Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al.

ClusterBootstrap

Analyze Clustered Data with Generalized Linear Models using the Cluster Bootstrap

clusterCons

Calculate the consensus clustering result from re-sampled clustering experiments with the option of using multiple algorithms and parameter

clusteredinterference

Causal Effects from Observational Studies with Clustered Interference

ClusteredMutations

Location and Visualization of Clustered Somatic Mutations

clusterExperiment

Compare Clusterings for Single-Cell Sequencing

clusterfly

Explore clustering interactively using R and GGobi

clustergas

A hierarchical clustering method based on genetic algorithms

clusterGeneration

Random Cluster Generation (with Specified Degree of Separation)

clusterGenomics

Identifying clusters in genomics data by recursive partitioning

clustering.sc.dp

Optimal Distance-Based Clustering for Multidimensional Data with Sequential Constraint

ClusterJudge

Judging Quality of Clustering Methods using Mutual Information

clustermq

Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM, PBS/Torque)

clusternomics

Integrative Clustering for Heterogeneous Biomedical Datasets

clusternor

A Parallel Clustering Non-Uniform Memory Access ('NUMA') Optimized Package

clusterPower

Power Calculations for Cluster-Randomized and Cluster-Randomized Crossover Trials

clusterProfiler

statistical analysis and visualization of functional profiles for genes and gene clusters

ClusterR

Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids and Affinity Propagation Clustering

clusterRepro

Reproducibility of Gene Expression Clusters

clusterSeq

Clustering of high-throughput sequencing data by identifying co-expression patterns

clusterSEs

Calculate Cluster-Robust p-Values and Confidence Intervals

ClusterSignificance

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data

clusterSim

Searching for Optimal Clustering Procedure for a Data Set

clusterStab

Compute cluster stability scores for microarray data

ClusterStability

Assessment of Stability of Individual Objects or Clusters in Partitioning Solutions

ClustGeo

Hierarchical Clustering with Spatial Constraints

clustMixType

k-Prototypes Clustering for Mixed Variable-Type Data

ClustMMDD

Variable Selection in Clustering by Mixture Models for Discrete Data

clustRcompaR

Easy Interface for Clustering a Set of Documents and Exploring Group- Based Patterns

clustrd

Methods for Joint Dimension Reduction and Clustering

clustree

Visualise Clusterings at Different Resolutions

CLUSTShiny

Interactive Document for Working with Cluster Analysis

ClustVarLV

Clustering of Variables Around Latent Variables

clustvarsel

Variable Selection for Gaussian Model-Based Clustering

ClusVis

Gaussian-Based Visualization of Gaussian and Non-Gaussian Model-Based Clustering

CMA

Synthesis of microarray-based classification

cmaes

Covariance Matrix Adapting Evolutionary Strategy

cmaesr

Covariance Matrix Adaptation Evolution Strategy

cMAP

A data package containing annotation data for cMAP

CMatching

Matching Algorithms for Causal Inference with Clustered Data

cmce

Computer Model Calibration for Deterministic and Stochastic Simulators

cmenet

Bi-Level Selection of Conditional Main Effects

cmna

Computational Methods for Numerical Analysis

cMonkey

cMonkey integrated biclustering algorithm

CMPControl

Control Charts for Conway-Maxwell-Poisson Distribution

cmprsk

Subdistribution Analysis of Competing Risks

cmprskContin

Continuous mark-specific relative risks for two groups

cmprskQR

Analysis of Competing Risks Using Quantile Regressions

cmrutils

Misc Functions of the Center for the Mathematical Research

cmvnorm

The Complex Multivariate Gaussian Distribution

cn.farms

cn.FARMS - factor analysis for copy number estimation

cn.mops

cn.mops - Mixture of Poissons for CNV detection in NGS data

cna

Causal Modeling with Coincidence Analysis

CNAnorm

A normalization method for Copy Number Aberration in cancer samples

cnbdistr

Conditional Negative Binomial Distribution

cncaGUI

Canonical Non-Symmetrical Correspondence Analysis in R

CNLTreg

Complex-Valued Wavelet Lifting for Signal Denoising

CNLTtsa

Complex-Valued Wavelet Lifting for Univariate and Bivariate Time Series Analysis

cnmlcd

Maximum Likelihood Estimation of a Log-Concave Density Function

CNORdt

Add-on to CellNOptR: Discretized time treatments

CNORfeeder

Integration of CellNOptR to add missing links

CNPBayes

Bayesian mixture models for copy number polymorphisms

CNprep

Pre-process DNA Copy Number (CN) Data for Detection of CN Events

CNTools

Convert segment data into a region by sample matrix to allow for other high level computational analyses.

CNull

Fast Algorithms for Frequency-Preserving Null Models in Ecology

CNVassoc

Association Analysis of CNV Data and Imputed SNPs

CNVassocData

Example data sets for association analysis of CNV data

cnvGSA

Gene Set Analysis of (Rare) Copy Number Variants

cnvGSAdata

Data used in the vignette of the cnvGSA package

CNVPanelizer

Reliable CNV detection in targeted sequencing applications

CNVrd2

CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

CNVScope

A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization

CNVtools

A package to test genetic association with CNV data

coalitions

Coalition Probabilities in Multi-Party Democracies

cobiclust

Biclustering via Latent Block Model Adapted to Overdispersed Count Data

cobindR

Finding Co-occuring motifs of transcription factor binding sites

cobs

Constrained B-Splines (Sparse Matrix Based)

cobs99

Constrained B-splines -- outdated 1999 version

CoCiteStats

Different test statistics based on co-citation.

COCONUT

COmbat CO-Normalization Using conTrols (COCONUT)

cocoreg

Extract Shared Variation in Collections of Data Sets Using Regression Models

cocron

Statistical Comparisons of Two or more Alpha Coefficients

coda

Output Analysis and Diagnostics for MCMC

coda.base

A Basic Set of Functions for Compositional Data Analysis

codadiags

Markov chain Monte Carlo burn-in based on "bridge" statistics

cOde

Automated C Code Generation for 'deSolve', 'bvpSolve'

codebook

Automatic Codebooks from Metadata Encoded in Dataset Attributes

CodeDepends

Analysis of R Code for Reproducible Research and Code Comprehension

codelink

Manipulation of Codelink microarray data

codemetar

Generate 'CodeMeta' Metadata for R Packages

CODEX

A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

codified

Produce Standard/Formalized Demographics Tables

CoDiNA

Co-Expression Differential Network Analysis

codingMatrices

Alternative Factor Coding Matrices for Linear Model Formulae

coefficientalpha

Robust Coefficient Alpha and Omega with Missing and Non-Normal Data

coenoflex

Gradient-Based Coenospace Vegetation Simulator

coexist

Species coexistence modeling and analysis

coexnet

coexnet: An R package to build CO-EXpression NETworks from Microarray Data

CoGAPS

Coordinated Gene Activity in Pattern Sets

cogena

co-expressed gene-set enrichment analysis

cogmapr

Cognitive Mapping Tools Based on Coding of Textual Sources

COHCAP

CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

COHCAPanno

Annotations for City of Hope CpG Island Analysis Pipeline

coin

Conditional Inference Procedures in a Permutation Test Framework

coindeskr

Access 'CoinDesk' Bitcoin Price Index API

coinmarketcapr

Get Cryptocurrencies Market Cap Prices from Coin Market Cap

CoinMinD

Simultaneous Confidence Interval for Multinomial Proportion

cointmonitoR

Consistent Monitoring of Stationarity and Cointegrating Relationships

cointReg

Parameter Estimation and Inference in a Cointegrating Regression

colbycol

Read big text files column by column, sometimes much bigger than available RAM, into R.

colcor

Tests for column correlation in the presence of row correlation

colf

Constrained Optimization on Linear Function

CollapseLevels

Collapses Levels, Computes Information Value and WoE

collapsibleTree

Interactive Collapsible Tree Diagrams using 'D3.js'

collectArgs

Quickly and Neatly Collect Arguments from One Environment to Pass to Another

collector

Quantified Risk Assessment Data Collection

CollessLike

Distribution and Percentile of Sackin, Cophenetic and Colless-Like Balance Indices of Phylogenetic Trees

collidr

Check for Namespace Collisions with Other Packages and Functions on CRAN

CollocInfer

Collocation Inference for Dynamic Systems

collpcm

Collapsed Latent Position Cluster Model for Social Networks

collUtils

Auxiliary Package for Package 'CollapsABEL'

colmozzie

Dengue Cases and Climate Variables in Colombo Sri Lanka

coloc

Colocalisation Tests of Two Genetic Traits

colocalization

Normalized Spatial Intensity Correlation

colocr

Conduct Co-Localization Analysis of Fluorescence Microscopy Images

colonCA

exprSet for Alon et al. (1999) colon cancer data

colordistance

Distance Metrics for Image Color Similarity

colorednoise

Simulate Temporally Autocorrelated Populations

colorfindr

Extract Colors from Windows BMP, JPEG, PNG, TIFF, and SVG Format Images

colorfulVennPlot

Plot and add custom coloring to Venn diagrams for 2-dimensional, 3-dimensional and 4-dimensional data.

colorhcplot

Colorful Hierarchical Clustering Dendrograms

colormap

Color Palettes using Colormaps Node Module

colorpatch

Optimized Rendering of Fold Changes and Confidence Values

colorplaner

A 'ggplot2' Extension to Visualize Two Variables per Color Aesthetic Through Color Space Projections

colorr

Color Palettes for EPL, MLB, NBA, NHL, and NFL Teams

colorspace

A Toolbox for Manipulating and Assessing Colors and Palettes

colorSpec

Color Calculations with Emphasis on Spectral Data

colortools

Tools for colors in a Hue-Saturation-Value (HSV) color model

colourpicker

A Colour Picker Tool for Shiny and for Selecting Colours in Plots

comato

Analysis of Concept Maps and Concept Landscapes

COMBAT

A Combined Association Test for Genes using Summary Statistics

COMBIA

Synergy/Antagonism Analyses of Drug Combinations

CombinePortfolio

Estimation of Optimal Portfolio Weights by Combining Simple Portfolio Strategies

CombinS

Construction Methods of some Series of PBIB Designs

coMET

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

cometExactTest

Exact Test from the Combinations of Mutually Exclusive Alterations (CoMEt) Algorithm

ComICS

Computational Methods for Immune Cell-Type Subsets

commentr

Print Nicely Formatted Comments for Use in Script Files

CommonJavaJars

Useful Libraries for Building a Java Based GUI under R

commonmark

High Performance CommonMark and Github Markdown Rendering in R

commonsMath

JAR Files of the Apache Commons Mathematics Library

CommonTrend

Extract and plot common trends from a cointegration system. Calculate P-value for Johansen Statistics.

CommT

Comparative Phylogeographic Analysis using the Community Tree Framework

comorbidities

Categorizes ICD-9-CM codes based on published comorbidity indices

compactr

Creates empty plots with compact axis notation

CompareCausalNetworks

Interface to Diverse Estimation Methods of Causal Networks

compareDF

Do a Git Style Diff of the Rows Between Two Dataframes with Similar Structure

compareODM

comparison of medical forms in CDISC ODM format

CompareTests

Correct for Verification Bias in Diagnostic Accuracy & Agreement

comparison

Multivariate likelihood ratio calculation and evaluation

compas

Conformational Manipulations of Protein Atomic Structures

COMPASS

Combinatorial Polyfunctionality Analysis of Single Cells

compboost

C++ Implementation of Component-Wise Boosting

compcodeR

RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

compeir

Event-specific incidence rates for competing risks data

compendiumdb

Tools for Retrieval and Storage of Functional Genomics Data

CompetingRisk

The Semi-Parametric Cumulative Incidence Function

CompGLM

Conway-Maxwell-Poisson GLM and Distribution Functions

CompGO

An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation

ComplexAnalysis

Numerically Evaluate Integrals and Derivatives (also Higher Order) of Vector- And Complex-Valued Functions

complexity

Calculate the Proportion of Permutations in Line with an Informative Hypothesis

complmrob

Robust Linear Regression with Compositional Data as Covariates

COMPoissonReg

Conway-Maxwell Poisson (COM-Poisson) Regression

compositionsGUI

Graphical User Environment for Compositional Data Analysis

compound.Cox

Univariate Feature Selection and Compound Covariate for Predicting Survival

CompQuadForm

Distribution Function of Quadratic Forms in Normal Variables

CompRandFld

Composite-Likelihood Based Analysis of Random Fields

comtradr

Interface with the United Nations Comtrade API

con2aqi

Calculate the AQI from Pollutant Concentration

concatenate

Human-Friendly Text from Unknown Strings

ConConPiWiFun

Optimisation with Continuous Convex Piecewise (Linear and Quadratic) Functions

concurve

Computes and Plots Consonance (Confidence) Intervals, P-Values, and S-Values to Form Consonance and Surprisal Functions

cond

Approximate Conditional Inference for Logistic and Loglinear Models

condGEE

Parameter estimation in conditional GEE for recurrent event gap times

CondIndTests

Nonlinear Conditional Independence Tests

condir

Computation of P Values and Bayes Factors for Conditioning Data

conditionz

Control How Many Times Conditions are Thrown

condmixt

Conditional Density Estimation with Neural Network Conditional Mixtures

CondReg

Condition Number Regularized Covariance Estimation

condSURV

Estimation of the Conditional Survival Function for Ordered Multivariate Failure Time Data

condusco

Query-Driven Pipeline Execution and Query Templates

condvis

Conditional Visualization for Statistical Models

condvis2

Conditional Visualization for Statistical Models

coneproj

Primal or Dual Cone Projections with Routines for Constrained Regression

conf

Visualization and Analysis of Statistical Measures of Confidence

confidence

Confidence Estimation of Environmental State Classifications

config

Manage Environment Specific Configuration Values

ConfigParser

Package to Parse an INI File, Including Variable Interpolation

configr

An Implementation of Parsing and Writing Configuration File (JSON/INI/YAML/TOML)

confinterpret

Descriptive Interpretations of Confidence Intervals

ConfIntVariance

Confidence Interval for the Univariate Population Variance without Normality Assumption

conflicted

An Alternative Conflict Resolution Strategy

conformal

Conformal Prediction for Regression and Classification

conformalClassification

Transductive and Inductive Conformal Predictions for Classification Problems

ConfoundedMeta

Sensitivity Analyses for Unmeasured Confounding in Meta-Analyses

confReg

Confidence Estimators for Individual Regression Predictions

confreq

Configural Frequencies Analysis Using Log-Linear Modeling

confSAM

Estimates and Bounds for the False Discovery Proportion, by Permutation

congressbr

Downloads, Unpacks and Tidies Legislative Data from the Brazilian Federal Senate and Chamber of Deputies

CongreveLamsdell2016

Distance Metrics for Trees Generated by Congreve and Lamsdell

conicfit

Algorithms for Fitting Circles, Ellipses and Conics Based on the Work by Prof. Nikolai Chernov

conjoint

An Implementation of Conjoint Analysis Method

ConjointChecks

A package to check the cancellation axioms of conjoint measurement.

connect3

A Tool for Reproducible Research by Converting 'LaTeX' Files Generated by R Sweave to Rich Text Format Files

ConnectivityMap

Functional connections between drugs, genes and diseases as revealed by common gene-expression changes

ConnMatTools

Tools for Working with Connectivity Data

conover.test

Conover-Iman Test of Multiple Comparisons Using Rank Sums

ConR

Computation of Parameters Used in Preliminary Assessment of Conservation Status

consensusOV

Gene expression-based subtype classification for high-grade serous ovarian cancer

consensusSeekeR

Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

ConSpline

Partial Linear Least-Squares Regression using Constrained Splines

ConsRank

Compute the Median Ranking(s) According to the Kemeny's Axiomatic Approach

constants

Reference on Constants, Units and Uncertainty

constellation

Identify Event Sequences Using Time Series Joins

constrainedKriging

Constrained, Covariance-Matching Constrained and Universal Point or Block Kriging

conStruct

Models Spatially Continuous and Discrete Population Genetic Structure

container

Deque, Set, and Dict - R6 Based Container Classes with Iterators

ContaminatedMixt

Model-Based Clustering and Classification with the Multivariate Contaminated Normal Distribution

contextual

Simulation and Analysis of Contextual Multi-Armed Bandit Policies

contiBAIT

Improves Early Build Genome Assemblies using Strand-Seq Data

contoureR

Contouring of Non-Regular Three-Dimensional Data

ContourFunctions

Create Contour Plots from Data or a Function

controlTest

Quantile Comparison for Two-Sample Right-Censored Survival Data

conumee

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

convexjlr

Disciplined Convex Programming in R using 'Convex.jl'

convey

Income Concentration Analysis with Complex Survey Samples

convoSPAT

Convolution-Based Nonstationary Spatial Modeling

cooccur

Probabilistic Species Co-Occurrence Analysis in R

coop

Co-Operation: Fast Covariance, Correlation, and Cosine Similarity Operations

CoopGame

Important Concepts of Cooperative Game Theory

coopProductGame

Cooperative Aspects of Linear Production Programming Problems

cooptrees

Cooperative aspects of optimal trees in weighted graphs

CoordinateCleaner

Automated Cleaning of Occurrence Records from Biological Collections

COP

Variables selection for index models via correlation pursuit

copa

Functions to perform cancer outlier profile analysis.

copas

Statistical methods to model and adjust for bias in meta-analysis

COPASutils

Tools for processing COPAS large-particle flow cytometer data

copBasic

General Bivariate Copula Theory and Many Utility Functions

copCAR

Fitting the copCAR Regression Model for Discrete Areal Data

CopCTS

Copula-Based Semiparametric Analysis for Time Series Data with Detection Limits

COPDSexualDimorphism.data

Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation.

cope

Coverage Probability Excursion (CoPE) Sets

coprimary

Sample Size Calculation for Two Primary Time-to-Event Endpoints in Clinical Trials

Copula.Markov

Copula-Based Estimation and Statistical Process Control for Serially Correlated Time Series

Copula.surv

Association Analysis of Bivariate Survival Data Based on Copulas

CopulaCenR

Copula-Based Regression Models for Bivariate Censored Data

CopulaDTA

Copula Based Bivariate Beta-Binomial Model for Diagnostic Test Accuracy Studies

copulaedas

Estimation of Distribution Algorithms Based on Copulas

CopulaRegression

Bivariate Copula Based Regression Models

CopulaREMADA

Copula Mixed Models for Multivariate Meta-Analysis of Diagnostic Test Accuracy Studies

CopyDetect

Computing Response Similarity Indices for Multiple-Choice Tests

copynumber

Segmentation of single- and multi-track copy number data by penalized least squares regression.

CopyNumber450k

R package for calling CNV from Illumina 450k methylation microarrays

CopyNumber450kCancer

Baseline Correction for Copy Number Data from Cancer Samples

CopyNumber450kData

Example data for the Illumina Methylation 450k array

CopywriteR

Copy number information from targeted sequencing using off-target reads

Corbi

Collection of Rudimentary Bioinformatics Tools

corcounts

Generate correlated count random variables

cord

Community Estimation in G-Models via CORD

coreCT

Programmatic Analysis of Sediment Cores Using Computed Tomography Imaging

CoRegNet

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

CoreGx

Classes and Functions to Serve as the Basis for Other 'Gx' Packages

CORElearn

Classification, Regression and Feature Evaluation

coreSim

Core Functionality for Simulating Quantities of Interest from Generalised Linear Models

coreTDT

TDT for compound heterozygous and recessive models

corlink

Record Linkage, Incorporating Imputation for Missing Agreement Patterns, and Modeling Correlation Patterns Between Fields

CORM

The Clustering of Regression Models Method

CorMut

Detect the correlated mutations based on selection pressure

CornerstoneR

Collection of Scripts for Interface Between 'Cornerstone' and 'R'

coroICA

Confounding Robust Independent Component Analysis for Noisy and Grouped Data

corpcor

Efficient Estimation of Covariance and (Partial) Correlation

corpora

Statistics and data sets for corpus frequency data

CoRpower

Power Calculations for Assessing Correlates of Risk in Clinical Efficacy Trials

corpustools

Managing, Querying and Analyzing Tokenized Text

corr2D

Implementation of 2D Correlation Analysis in R

CorrBin

Nonparametrics with Clustered Binary and Multinomial Data

corrDNA

Finding Associations in Position-Wise Aligned DNA Sequence Dataset

CorrectOverloadedPeaks

Correct Overloaded Peaks from GC-APCI-MS Data

CorReg

Linear Regression Based on Linear Structure Between Variables

corregp

Functions and Methods for Correspondence Regression

correlate

Multivariate Data Generation by Permutation

Correlplot

A collection of functions for graphing correlation matrices

CORREP

Multivariate Correlation Estimator and Statistical Inference Procedures.

CorrMixed

Estimate Correlations Between Repeatedly Measured Endpoints (E.g., Reliability) Based on Linear Mixed-Effects Models

corrperm

Permutation Tests of Correlation with Repeated Measurements

CorrToolBox

Modeling Correlational Magnitude Transformations in Discretization Contexts

corset

Arbitrary Bounding of Series and Time Series Objects

CorShrink

Adaptive Shrinkage of Correlation and Covariance Matrices

corTools

Tools for processing data after a Genome Wide Association Study

cosa

Bound Constrained Optimal Sample Allocation

CoSeg

Cosegregation Analysis and Pedigree Simulation

coseq

Co-Expression Analysis of Sequencing Data

cosinor

Tools for estimating and predicting the cosinor model

cosinor2

Extended Tools for Cosinor Analysis of Rhythms

cosmiq

cosmiq - COmbining Single Masses Into Quantities

cosmoFns

Functions for cosmological distances, times, luminosities, etc.

CosmoPhotoz

Photometric redshift estimation using generalized linear models

COSNet

Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings

cosso

Fit Regularized Nonparametric Regression Models Using COSSO Penalty.

COST

Copula-Based Semiparametric Models for Spatio-Temporal Data

costat

Time Series Costationarity Determination

costsensitive

Cost-Sensitive Multi-Class Classification

cottonprobe

Probe sequence data for microarrays of type cotton

couchDB

Connect to and Work with CouchDB Databases

CountClust

Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models

countcolors

Locates and Counts Pixels Within Color Range(s) in Images

Counterfactual

Estimation and Inference Methods for Counterfactual Analysis

countfitteR

Comprehensive Automatized Evaluation of Distribution Models for Count Data

countgmifs

Discrete Response Regression for High-Dimensional Data

countHMM

Penalized Estimation of Flexible Hidden Markov Models for Time Series of Counts

Countr

Flexible Univariate Count Models Based on Renewal Processes

CountsEPPM

Mean and Variance Modeling of Count Data

countToFPKM

Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)

countTransformers

Transform Counts in RNA-Seq Data Analysis

countyfloods

Quantify United States County-Level Flood Measurements

countytimezones

Convert from UTC to Local Time for United States Counties

countyweather

Compiles Meterological Data for U.S. Counties

COUSCOus

A Residue-Residue Contact Detecting Method

covafillr

Local Polynomial Regression of State Dependent Covariates in State-Space Models

covatest

Tests on Properties of Space-Time Covariance Functions

covBM

Brownian Motion Processes for 'nlme'-Models

covEB

Empirical Bayes estimate of block diagonal covariance matrices

coveffectsplot

Produce Forest Plots to Visualize Covariate Effects

covequal

Test for Equality of Covariance Matrices

covLCA

Latent Class Models with Covariate Effects on Underlying and Measured Variables

covreg

A simultaneous regression model for the mean and covariance

covRNA

Multivariate Analysis of Transcriptomic Data

covRobust

Robust Covariance Estimation via Nearest Neighbor Cleaning

CovSelHigh

Model-Free Covariate Selection in High Dimensions

covsep

Tests for Determining if the Covariance Structure of 2-Dimensional Data is Separable

covTest

Computes covariance test for adaptive linear modelling

CovTools

Statistical Tools for Covariance Analysis

cowbell

Performs Segmented Linear Regression on Two Independent Variables

cowplot

Streamlined Plot Theme and Plot Annotations for 'ggplot2'

cowsay

Messages, Warnings, Strings with Ascii Animals

CoxBoost

Cox models by likelihood based boosting for a single survival endpoint or competing risks

coxed

Duration-Based Quantities of Interest for the Cox Proportional Hazards Model

coxinterval

Cox-Type Models for Interval-Censored Data

coxphf

Cox Regression with Firth's Penalized Likelihood

CoxPhLb

Analyzing Right-Censored Length-Biased Data

coxphMIC

Sparse Estimation of Cox Proportional Hazards Models via Approximated Information Criterion

coxphSGD

Stochastic Gradient Descent log-Likelihood Estimation in Cox Proportional Hazards Model

CoxPlus

Cox Regression (Proportional Hazards Model) with Multiple Causes and Mixed Effects

coxrt

Cox Proportional Hazards Regression for Right Truncated Data

cpa

Confirmatory Path Analysis through the d-sep tests

CPBayes

Bayesian Meta Analysis for Studying Cross-Phenotype Genetic Associations

cpca

Methods to perform Common Principal Component Analysis (CPCA)

cPCG

Efficient and Customized Preconditioned Conjugate Gradient Method for Solving System of Linear Equations

CpDyna

Change Point Detection in Dynamic Graphs

CPE

Concordance Probability Estimates in Survival Analysis

CpGassoc

Association Between Methylation and a Phenotype of Interest

cpgen

Parallelized Genomic Prediction and GWAS

CpGFilter

CpG Filtering Method Based on Intra-Class Correlation Coefficients

CPHshape

Find the maximum likelihood estimator of the shape constrained hazard baseline and the effect parameters in the Cox proportional hazards model

cpm

Sequential and Batch Change Detection Using Parametric and Nonparametric Methods

CPMCGLM

Correction of the P-Value after Multiple Coding in Generalized Linear Models

CPP

Composition of Probabilistic Preferences (CPP)

cppRouting

Fast Implementation of Dijkstra Algorithm

Cprob

The Conditional Probability Function of a Competing Event

cprr

Functions for Working with Danish CPR Numbers

CPsurv

Nonparametric Change Point Estimation for Survival Data

cpsurvsim

Simulating Survival Data from Change-Point Hazard Distributions

cpvSNP

Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

cqrReg

Quantile, Composite Quantile Regression and Regularized Versions

cquad

Conditional Maximum Likelihood for Quadratic Exponential Models for Binary Panel Data

CR

Power Calculation for Weighted Log-Rank Tests in Cure Rate Models

cr17

Testing Differences Between Competing Risks Models and Their Visualisations

crackR

Probabilistic damage tolerance analysis for fatigue cracking of metallic aerospace structures

cramer

Multivariate Nonparametric Cramer-Test for the Two-Sample-Problem

CramTest

Univariate Cramer Test on Two Samples of Data

cranlogs

Download Logs from the 'RStudio' 'CRAN' Mirror

cranly

Package Directives and Collaboration Networks in CRAN

CRANsearcher

RStudio Addin for Searching Packages in CRAN Database Based on Keywords

crantastic

Various R tools for http://crantastic.org/

crawl

Fit Continuous-Time Correlated Random Walk Models to Animal Movement Data

crblocks

Categorical Randomized Block Data Analysis

crch

Censored Regression with Conditional Heteroscedasticity

CREAM

Clustering of Genomic Regions Analysis Method

credentials

Tools for Managing SSH and Git Credentials

CreditMetrics

Functions for calculating the CreditMetrics risk model

creditmodel

Build Binary Classification Models in One Integrated Offering

CreditRisk

Evaluation of Credit Risk with Structural and Reduced Form Models

cregg

Simple Conjoint Tidying, Analysis, and Visualization

cRegulome

Obtain and Visualize Regulome-Gene Expression Correlations in Cancer

CRFCSD

Mixture Cure Generalized Odds Ratio Frailty Models for Clustered Current Status Data

crfsuite

Conditional Random Fields for Labelling Sequential Data in Natural Language Processing

cricketr

Analyze Cricketers and Cricket Teams Based on ESPN Cricinfo Statsguru

CRImage

CRImage a package to classify cells and calculate tumour cellularity

crimCV

Group-Based Modelling of Longitudinal Data

crimedata

Access Crime Data from the Open Crime Database

crimelinkage

Statistical Methods for Crime Series Linkage

crisp

Fits a Model that Partitions the Covariate Space into Blocks in a Data- Adaptive Way

CRISPRseek

Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

CrispRVariants

Tools for counting and visualising mutations in a target location

crlmm

Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

CRM

Continual Reassessment Method (CRM) for Phase I Clinical Trials

crminer

Fetch 'Scholary' Full Text from 'Crossref'

crmn

CCMN and other noRMalizatioN methods for metabolomics data

crmPack

Object-Oriented Implementation of CRM Designs

crn

Downloads and Builds datasets for Climate Reference Network

crochet

Implementation Helper for '[' and '[<-' of Custom Matrix-Like Types

cromwellDashboard

A Dashboard to Visualize Scientific Workflows in 'Cromwell'

cronR

Schedule R Scripts and Processes with the 'cron' Job Scheduler

cropdatape

Open Data of Agricultural Production of Crops of Peru

crossmeta

Cross Platform Meta-Analysis of Microarray Data

Crossover

Analysis and Search of Crossover Designs

crossReg

Confidence intervals for crossover points of two simple regression lines

crossrun

Joint Distribution of Number of Crossings and Longest Run

CrossScreening

Cross-Screening in Observational Studies that Test Many Hypotheses

crosstalk

Inter-Widget Interactivity for HTML Widgets

CrossVA

Verbal Autopsy Data Transformation for InSilicoVA and InterVA5 Algorithms

CrossValidate

Classes and Methods for Cross Validation of "Class Prediction" Algorithms

crosswalkr

Rename and Encode Data Frames Using External Crosswalk Files

crov

Constrained Regression Model for an Ordinal Response and Ordinal Predictors

CRPClustering

Bayesian Nonparametric Chinese Restaurant Process Clustering with Entropy

crqa

Cross-Recurrence Quantification Analysis for Categorical and Continuous Time-Series

crqanlp

Cross-Recurrence Quantification Analysis for Dynamic Natural Language Processing

crrp

Penalized Variable Selection in Competing Risks Regression

crrSC

Competing risks regression for Stratified and Clustered data

crrstep

Stepwise Covariate Selection for the Fine & Gray Competing Risks Regression Model

crseEventStudy

A Robust and Powerful Test of Abnormal Stock Returns in Long-Horizon Event Studies

crsnls

Nonlinear Regression Parameters Estimation by 'CRS4HC' and 'CRS4HCe'

crsra

Tidying and Analyzing 'Coursera' Research Export Data

CRTgeeDR

Doubly Robust Inverse Probability Weighted Augmented GEE Estimator

CRTSize

Sample Size Estimation Functions for Cluster Randomized Trials

cruts

Interface to Climatic Research Unit Time-Series Version 3.21 Data

CRWRM

Changing the Reference Group without Re-Running the Model

CrypticIBDcheck

Identifying Cryptic Relatedness in Genetic Association Studies

CryptRndTest

Statistical Tests for Cryptographic Randomness

cryst

Calculate the Relative Crystallinity of Starch by XRD and FTIR

csabounds

Bounds on Distributional Treatment Effect Parameters

csampling

Functions for Conditional Simulation in Regression-Scale Models

CSAR

Statistical tools for the analysis of ChIP-seq data

CSeqpat

Frequent Contiguous Sequential Pattern Mining of Text

CSESA

CRISPR-Based Salmonella Enterica Serotype Analyzer

CSFA

Connectivity Scores with Factor Analysis

cSFM

Covariate-adjusted Skewed Functional Model (cSFM)

cslogistic

Conditionally Specified Logistic Regression

csound

Accessing Csound functionality through R

csp

Correlates of State Policy Data Set in R

csrplus

Methods to Test Hypotheses on the Distribution of Spatial Point Processes

CSS

Extract information from an html document with CSS selectors

csSAM

csSAM - cell-specific Significance Analysis of Microarrays

cstab

Selection of Number of Clusters via Normalized Clustering Instability

cstar

Substantive significance testing for regression estimates and marginal effects.

CSTools

Assessing Skill of Climate Forecasts on Seasonal-to-Decadal Timescales

csv

Read and Write CSV Files with Selected Conventions

csvy

Import and Export CSV Data with a YAML Metadata Header

CTAShiny

Interactive Application for Working with Contingency Tables

CTDquerier

Package for CTDbase data query, visualization and downstream analysis

cthreshER

Continuous Threshold Expectile Regression

ctl

Correlated Trait Locus (CTL) Mapping in R

CTM

A Text Mining Toolkit for Chinese Document

ctmcd

Estimating the Parameters of a Continuous-Time Markov Chain from Discrete-Time Data

ctmcmove

Modeling Animal Movement with Continuous-Time Discrete-Space Markov Chains

ctmle

Collaborative Targeted Maximum Likelihood Estimation

ctqr

Censored and Truncated Quantile Regression

ctrdata

Retrieve and Analyze Information on Clinical Trials from Public Registers

ctrlGene

Assess the Stability of Candidate Housekeeping Genes

ctsem

Continuous Time Structural Equation Modelling

ctsGE

Clustering of Time Series Gene Expression data

CTShiny

Interactive Document for Working with Classification Tree Analysis

CUB

A Class of Mixture Models for Ordinal Data

cubature

Adaptive Multivariate Integration over Hypercubes

Cubist

Rule- And Instance-Based Regression Modeling

CuCubes

MultiDimensional Feature Selection (MDFS)

cudaBayesreg

CUDA Parallel Implementation of a Bayesian Multilevel Model for fMRI Data Analysis

cudaBayesregData

Data sets for the examples used in the package "cudaBayesreg"

CUFF

Charles's Utility Function using Formula

cultevo

Tools, Measures and Statistical Tests for Cultural Evolution

cummeRbund

Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

CUMP

Analyze Multivariate Phenotypes by Combining Univariate Results

cumplyr

Extends ddply to allow calculation of cumulative quantities.

cumSeg

Change Point Detection in Genomic Sequences

curatedBreastData

Curated breast cancer gene expression data with survival and treatment information

curatedCRCData

Colorectal Cancer Gene Expression Analysis

curatedMetagenomicData

Curated Metagenomic Data of the Human Microbiome

curatedOvarianData

Clinically Annotated Data for the Ovarian Cancer Transcriptome

curatedTCGAData

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

curlconverter

Tools to Transform 'cURL' Command-Line Calls to 'httr' Requests

curry

Partial Function Application with %<%, %-<%, and %><%

curstatCI

Confidence Intervals for the Current Status Model

curvecomp

Multiple Curve Comparisons Using Parametric Bootstrap

curveDepth

Tukey Curve Depth and Distance in the Space of Curves

The package will formally test two curves represented by discrete data sets to be statistically equal or not when the errors of the two curves were assumed either equal or not using the tube formula to calculate the tail probabilities.

curvHDR

Filtering of Flow Cytometry Samples

cusp

Cusp-Catastrophe Model Fitting Using Maximum Likelihood

CustomerScoringMetrics

Evaluation Metrics for Customer Scoring Models Depending on Binary Classifiers

customizedTraining

Customized Training for Lasso and Elastic-Net Regularized Generalized Linear Models

customLayout

Arrange Elements on the R's Drawing Area or Inside the PowerPoint's Slide

customProDB

Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

customsteps

Customizable Higher-Order Recipe Step Functions

cusum

CUSUM Charts for Monitoring of Hospital Performance

CUSUMdesign

Compute Decision Interval and Average Run Length for CUSUM Charts

cutoffR

CUTOFF: A Spatio-temporal Imputation Method

cutpointr

Determine and Evaluate Optimal Cutpoints in Binary Classification Tasks

CutpointsOEHR

Optimal Equal-HR Method to Find Two Cutpoints for U-Shaped Relationships in Cox Model

cuttlefish.model

An R package to perform LPUE standardization and stock assessment of the English Channel cuttlefish stock using a two-stage biomass model

cvar

Compute Expected Shortfall and Value at Risk for Continuous Distributions

cvAUC

Cross-Validated Area Under the ROC Curve Confidence Intervals

CVcalibration

Estimation of the Calibration Equation with Error-in Observations

cvcrand

Efficient Design and Analysis of Cluster Randomized Trials

CVD

Color Vision Deficiencies

CVE

Cancer Variant Explorer

cvequality

Tests for the Equality of Coefficients of Variation from Multiple Groups

CVglasso

Lasso Penalized Precision Matrix Estimation

CvM2SL1Test

L1-version of Cramer-von Mises Two Sample Tests

CvM2SL2Test

Cramer-von Mises Two Sample Tests

cvmgof

Cramer-von Mises Goodness-of-Fit Tests

cvplogistic

Penalized Logistic Regression Model using Majorization Minimization by Coordinate Descent (MMCD) Algorithm

cvq2

Calculate the predictive squared correlation coefficient

CVR

Canonical Variate Regression

CVST

Fast Cross-Validation via Sequential Testing

CVThresh

Level-Dependent Cross-Validation Thresholding

cvTools

Cross-validation tools for regression models

CVTuningCov

Regularized Estimators of Covariance Matrices with CV Tuning

cvxbiclustr

Convex Biclustering Algorithm

cvxclustr

Splitting methods for convex clustering

CVXR

Disciplined Convex Optimization

cwhmisc

Miscellaneous Functions for Math, Plotting, Printing, Statistics, Strings, and Tools

cwm

Cluster Weighted Models by EM algorithm

cxhull

Convex Hull

cxxfunplus

extend cxxfunction by saving the dynamic shared objects

cycle

Significance of periodic expression pattern in time-series data

cycleRtools

Tools for Cycling Data Analysis

cyclestreets

Cycle Routing and Data for Cycling Advocacy

cyclocomp

Cyclomatic Complexity of R Code

cycloids

cyclones

Cyclone identification

Cyclops

Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis

cydar

Using Mass Cytometry for Differential Abundance Analyses

cymruservices

Query 'Team Cymru' 'IP' Address, Autonomous System Number ('ASN'), Border Gateway Protocol ('BGP'), Bogon and 'Malware' Hash Data Services

cyp450cdf

cyphid

Cycle and Phase Identification for mastication data

cyphr

High Level Encryption Wrappers

cystiSim

Agent-Based Model for Taenia_solium Transmission and Control

CytobankAPI

Cytobank API Wrapper for R

CytobankAPIstats

Computes Signaling and Population Stats for Cytometry Data on Cytobank using 'CytobankAPI'

CytobankBridgeR

Bridging and Extending the CytobankAPI Package in R to the Cytobank Web Application

cytoDiv

Cytometric diversity indices

CytoDx

Robust prediction of clinical outcomes using cytometry data without cell gating

cytofan

Plot Fan Plots for Cytometry Data using 'ggplot2'

cytofkit

cytofkit: an integrated mass cytometry data analysis pipeline

cytolib

C++ infrastructure for representing and interacting with the gated cytometry

cytometree

Automated Cytometry Gating and Annotation

cytominer

Methods for Image-Based Cell Profiling

CytoML

GatingML interface for openCyto

Packages

c060

c14bazAAR

c212

c2c

c3

c3net

C443

C50

ca

cablecuttr

cabootcrs

cacher

cacheSweave

cacIRT

CaDENCE

CADFtest

CADStat

caesar

CAFE

caffsim

CAGEfightR

CAGEr

CAGExploreR

caGUI

cAIC4

CAinterprTools

Cairo

cairoDevice