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List of libraries in RError(s), warning(s): Warning message: In library() : library ‘/usr/local/lib/R/site-library’ contains no packages Packages in library ‘/usr/lib/R/site-library’:
abind Combine Multidimensional Arrays
acepack ace() and avas() for selecting regression
transformations
ade4 Analysis of Ecological Data : Exploratory and
Euclidean Methods in Environmental Sciences
afex Analysis of Factorial Experiments
affy Methods for Affymetrix Oligonucleotide Arrays
affyio Tools for parsing Affymetrix data files
altcdfenvs alternative CDF environments (aka probeset
mappings)
Amelia A Program for Missing Data
AMORE A MORE flexible neural network package
annotate Annotation for microarrays
AnnotationDbi Annotation Database Interface
ape Analyses of Phylogenetics and Evolution
aroma.light Light-Weight Methods for Normalization and
Visualization of Microarray Data using Only
Basic R Data Types
base64enc Tools for base64 encoding
BatchJobs Batch Computing with R
BayesFactor Computation of Bayes Factors for Common Designs
bayesm Bayesian Inference for
Marketing/Micro-Econometrics
BBmisc Miscellaneous Helper Functions for B. Bischl
beeswarm The Bee Swarm Plot, an Alternative to
Stripchart
BiasedUrn Biased Urn model distributions
bio3d Biological Structure Analysis
Biobase Biobase: Base functions for Bioconductor
BiocGenerics S4 generic functions for Bioconductor
BiocInstaller Install/Update Bioconductor and CRAN Packages
BiocParallel Bioconductor facilities for parallel evaluation
biomaRt Interface to BioMart databases (e.g. Ensembl,
COSMIC ,Wormbase and Gramene)
Biostrings String objects representing biological
sequences, and matching algorithms
biovizBase Basic graphic utilities for visualization of
genomic data.
bitops Bitwise Operations
blockmodeling An R package for Generalized and classical
blockmodeling of valued networks
BMS Bayesian Model Averaging Library
BoolNet Construction, Simulation and Analysis of
Boolean Networks
BradleyTerry2 Bradley-Terry Models
brew Templating Framework for Report Generation
brglm Bias reduction in binomial-response generalized
linear models.
BSgenome Infrastructure for Biostrings-based genome data
packages and support for efficient SNP
representation
cairoDevice Embeddable Cairo Graphics Device Driver
car Companion to Applied Regression
caret Classification and Regression Training
caTools Tools: moving window statistics, GIF, Base64,
ROC AUC, etc.
checkmate Fast and Versatile Argument Checks
chron Chronological Objects which can Handle Dates
and Times
cmprsk Subdistribution Analysis of Competing Risks
coda Output Analysis and Diagnostics for MCMC
coin Conditional Inference Procedures in a
Permutation Test Framework
colorspace Color Space Manipulation
combinat combinatorics utilities
contfrac Continued fractions
conting Bayesian Analysis of Contingency Tables
crayon Colored Terminal Output
cubature Adaptive multivariate integration over
hypercubes
cummeRbund Analysis, exploration, manipulation, and
visualization of Cufflinks high-throughput
sequencing data.
date Functions for handling dates
DBI R Database Interface
deal Learning Bayesian Networks with Mixed Variables
deldir Delaunay Triangulation and Dirichlet (Voronoi)
Tessellation
DEoptimR Differential Evolution Optimization in Pure R
deSolve Solvers for Initial Value Problems of
Differential Equations (ODE, DAE, DDE)
DiagnosisMed Diagnostic test accuracy evaluation for medical
professionals.
dichromat Color Schemes for Dichromats
digest Create Compact Hash Digests of R Objects
doMC Foreach Parallel Adaptor for 'parallel'
doParallel Foreach parallel adaptor for the parallel
package
DoseFinding Planning and Analyzing Dose Finding Experiments
doSNOW Foreach Parallel Adaptor for the 'snow' Package
downloader A package for downloading files over http and
https
e1071 Misc Functions of the Department of Statistics,
Probability Theory Group (Formerly: E1071), TU
Wien
EBSeq An R package for gene and isoform differential
expression analysis of RNA-seq data
eco Ecological Inference in 2x2 Tables
ecodist Dissimilarity-based functions for ecological
analysis
edgeR Empirical analysis of digital gene expression
data in R
effects Effect Displays for Linear, Generalized Linear,
and Other Models
elliptic elliptic functions
energy E-statistics (energy statistics)
Epi A Package for Statistical Analysis in
Epidemiology
epibasix Elementary Epidemiological Functions for
Epidemiology and Biostatistics
epicalc Epidemiological calculator
epiR Tools for the Analysis of Epidemiological Data
epitools Epidemiology Tools
eRm Extended Rasch Modeling.
estimability Tools for Assessing Estimability of Linear
Predictions
etm Empirical Transition Matrix
evaluate Parsing and evaluation tools that provide more
details than the default.
evd Functions for extreme value distributions
expm Matrix exponential
fail File Abstraction Interface Layer (FAIL)
fAsianOptions EBM and Asian Option Valuation
fAssets Rmetrics - Analysing and Modelling Financial
Assets
fastcluster Fast Hierarchical Clustering Routines for R and
Python
fastmatch Fast match() function
fBasics Rmetrics - Markets and Basic Statistics
fBonds Bonds and Interest Rate Models
fCopulae Rmetrics - Bivariate Dependence Structures with
Copulae
fExoticOptions Exotic Option Valuation
fExtremes Rmetrics - Extreme Financial Market Data
fGarch Rmetrics - Autoregressive Conditional
Heteroskedastic Modelling
fImport Rmetrics - Economic and Financial Data Import
fMultivar Rmetrics - Analysing and Modeling Multivariate
Financial Return Distributions
fNonlinear Nonlinear and Chaotic Time Series Modelling
fOptions Rmetrics - Pricing and Evaluating Basic Options
foreach Provides Foreach Looping Construct for R
formatR Format R Code Automatically
Formula Extended Model Formulas
fPortfolio Rmetrics - Portfolio Selection and Optimization
fRegression Rmetrics - Regression Based Decision and
Prediction
fTrading Technical Trading Analysis
fUnitRoots Trends and Unit Roots
futile.logger A Logging Utility for R
futile.options Futile options management
gam Generalized Additive Models
gbm Generalized Boosted Regression Models
gdata Various R Programming Tools for Data
Manipulation
g.data Delayed-Data Packages
geepack Generalized Estimating Equation Package
GenABEL genome-wide SNP association analysis
GenABEL.data Package contains data which is used by GenABEL
example and test functions
genefilter genefilter: methods for filtering genes from
high-throughput experiments
genetics Population Genetics
GenomeInfoDb Utilities for manipulating chromosome and other
'seqname' identifiers
GenomicAlignments Representation and manipulation of short
genomic alignments
GenomicFeatures Tools for making and manipulating transcript
centric annotations
GenomicRanges Representation and manipulation of genomic
intervals and variables defined along a genome
getopt C-like getopt behavior.
ggplot2 An Implementation of the Grammar of Graphics
gmaps Wrapper and auxilliary functions for maps
package to work with grid graphics system.
gmodels Various R Programming Tools for Model Fitting
gnm Generalized Nonlinear Models
gplots Various R Programming Tools for Plotting Data
graph graph: A package to handle graph data
structures
gregmisc Greg's Miscellaneous Functions
gridExtra Miscellaneous Functions for "Grid" Graphics
gsl wrapper for the Gnu Scientific Library
gss General Smoothing Splines
gtable Arrange grobs in tables.
gtools Various R Programming Tools
Gviz Plotting data and annotation information along
genomic coordinates
haplo.stats Statistical Analysis of Haplotypes with Traits
and Covariates when Linkage Phase is Ambiguous
hdf5 HDF5
HilbertVis Hilbert curve visualization
Hmisc Harrell Miscellaneous
httpuv HTTP and WebSocket Server Library
hwriter HTML Writer - Outputs R objects in HTML format
hypergeo The Gauss Hypergeometric Function
hypergraph A package providing hypergraph data structures
igraph Network analysis and visualization
inline Functions to Inline C, C++, Fortran Function
Calls from R
int64 64 bit integer types
IRanges Infrastructure for manipulating intervals on
sequences
iterators Provides Iterator Construct for R
its Irregular Time Series
jsonlite A Robust, High Performance JSON Parser and
Generator for R
kernlab Kernel-Based Machine Learning Lab
labeling Axis Labeling
lambda.r Modeling Data with Functional Programming
latticeExtra Extra Graphical Utilities Based on Lattice
LearnBayes Functions for Learning Bayesian Inference
lhs Latin Hypercube Samples
limma Linear Models for Microarray Data
littler R at the Command-Line via 'r'
lme4 Linear Mixed-Effects Models using 'Eigen' and
S4
lmtest Testing Linear Regression Models
logspline Logspline Density Estimation Routines
lpSolve Interface to 'Lp_solve' v. 5.5 to Solve
Linear/Integer Programs
lsmeans Least-Squares Means
magrittr A Forward-Pipe Operator for R
makecdfenv CDF Environment Maker
MALDIquant Quantitative Analysis of Mass Spectrometry Data
MALDIquantForeign Import/Export routines for MALDIquant
mapdata Extra Map Databases
mapproj Map Projections
maps Draw Geographical Maps
MatchIt MatchIt: Nonparametric Preprocessing for
Parametric Casual Inference
MatrixModels Modelling with Sparse And Dense Matrices
matrixStats Methods that Apply to Rows and Columns of
Matrices (and to Vectors)
maxLik Maximum Likelihood Estimation
MCMCpack Markov chain Monte Carlo (MCMC) Package
medAdherence Medication Adherence: Commonly Used Definitions
memoise Memoise functions
mFilter Miscellaneous time series filters
mime Map Filenames to MIME Types
minqa Derivative-free optimization algorithms by
quadratic approximation
misc3d Miscellaneous 3D Plots
miscTools Miscellaneous Tools and Utilities
mixtools Tools for analyzing finite mixture models
mnormt The Multivariate Normal and t Distributions
MNP R Package for Fitting the Multinomial Probit
Model
modeltools Tools and Classes for Statistical Models
msm Multi-State Markov and Hidden Markov Models in
Continuous Time
multcomp Simultaneous Inference in General Parametric
Models
multicore A stub package to ease transition to
'parallel'.
multtest Resampling-based multiple hypothesis testing
munsell Munsell colour system
mvnormtest Normality test for multivariate variables
mvtnorm Multivariate Normal and t Distributions
ncdf4 Interface to Unidata netCDF (Version 4 or
Earlier) Format Data Files
nloptr R interface to NLopt
nnls The Lawson-Hanson algorithm for non-negative
least squares (NNLS)
numDeriv Accurate Numerical Derivatives
nws R functions for NetWorkSpaces and Sleigh
optparse Command line option parser.
pbapply Adding Progress Bar to '*apply' Functions
pbivnorm Vectorized Bivariate Normal CDF
pbkrtest Parametric Bootstrap and Kenward Roger Based
Methods for Mixed Model Comparison
permute Functions for generating restricted
permutations of data
phangorn Phylogenetic Analysis in R
pkgKitten Create Simple Packages Which Do not Upset R
Package Checks
plotrix Various Plotting Functions
plyr Tools for Splitting, Applying and Combining
Data
polspline Polynomial Spline Routines
polyclip Polygon Clipping
polyCub Cubature over Polygonal Domains
praise Praise Users
preprocessCore A collection of pre-processing functions
profileModel Tools for profiling inference functions for
various model classes
proto Prototype object-based programming
pscl Political Science Computational Laboratory,
Stanford University
psy Various procedures used in psychometry
pvclust Hierarchical Clustering with P-Values via
Multiscale Bootstrap Resampling
pwt Penn World Table (Versions 5.6, 6.x, 7.x)
pwt8 Penn World Table (Version 8.x)
qtl Tools for Analyzing QTL Experiments
quadprog Functions to solve Quadratic Programming
Problems.
quantreg Quantile Regression
qvalue Q-value estimation for false discovery rate
control
qvcalc Quasi Variances for Factor Effects in
Statistical Models
RandomFields Simulation and Analysis of Random Fields
randomForest Breiman and Cutler's Random Forests for
Classification and Regression
RaschSampler Rasch Sampler
Rcmdr R Commander
RcmdrMisc R Commander Miscellaneous Functions
RColorBrewer ColorBrewer Palettes
Rcpp Seamless R and C++ Integration
RcppArmadillo 'Rcpp' Integration for the 'Armadillo'
Templated Linear Algebra Library
RcppEigen 'Rcpp' Integration for the 'Eigen' Templated
Linear Algebra Library
RCurl General Network (HTTP/FTP/...) Client Interface
for R
readBrukerFlexData Reads Mass Spectrometry Data in Bruker *flex
Format
readMzXmlData Reads Mass Spectrometry Data in mzXML Format
readxl Read Excel Files
relimp Relative Contribution of Effects in a
Regression Model
reshape Flexibly reshape data.
reshape2 Flexibly reshape data: a reboot of the reshape
package.
rggobi Interface between R and GGobi
rgl 3D Visualization Using OpenGL
Rglpk R/GNU Linear Programming Kit Interface
RGtk2 R bindings for Gtk 2.8.0 and above
RInside C++ Classes to Embed R in C++ Applications
rjags Bayesian Graphical Models using MCMC
rJava Low-Level R to Java Interface
rjson JSON for R
R.methodsS3 S3 Methods Simplified
Rmpi Interface (Wrapper) to MPI (Message-Passing
Interface)
rms Regression Modeling Strategies
RMySQL Database Interface and 'MySQL' Driver for R
rneos rneos: XML-RPC Interface to NEOS
RNetCDF R Interface to NetCDF Datasets
Rniftilib R Interface to nifticlib for Reading and
Writing Images in NIfTI-1 and ANALYZE Format
robustbase Basic Robust Statistics
ROCR Visualizing the Performance of Scoring
Classifiers
RODBC ODBC Database Access
R.oo R Object-Oriented Programming with or without
References
RPostgreSQL R interface to the PostgreSQL database system
RQuantLib R Interface to the 'QuantLib' Library
Rsamtools Binary alignment (BAM), FASTA, variant call
(BCF), and tabix file import
RSclient Client for Rserve
rsdmx Tools for Reading SDMX Data and Metadata
Rserve Binary R server
Rsolnp General Non-linear Optimization
rsprng R interface to SPRNG (Scalable Parallel Random
Number Generators)
RSQLite SQLite Interface for R
Rsymphony SYMPHONY in R
rtracklayer R interface to genome browsers and their
annotation tracks
RUnit R Unit Test Framework
R.utils Various Programming Utilities
S4Vectors S4 implementation of vectors and lists
sandwich Robust Covariance Matrix Estimators
scales Scale Functions for Visualization
scatterplot3d 3D Scatter Plot
segmented Segmented relationships in regression models
with breakpoints/changepoints estimation
sendmailR send email using R
seqinr Biological Sequences Retrieval and Analysis
seroincidence Estimating Infection Rates from Serological
Data
ShortRead FASTQ input and manipulation
slam Sparse Lightweight Arrays and Matrices
sm Smoothing methods for nonparametric regression
and density estimation
sn The Skew-Normal and Skew-t Distributions
snow Simple Network of Workstations
snpStats SnpMatrix and XSnpMatrix classes and methods
sp classes and methods for spatial data
spam SPArse Matrix
SparseM Sparse Linear Algebra
spatstat Spatial Point Pattern analysis, model-fitting,
simulation, tests
spc Statistical Process Control -- Collection of
Some Useful Functions
stabledist Stable Distribution Functions
statmod Statistical Modeling
stringi Character String Processing Facilities
stringr Simple, Consistent Wrappers for Common String
Operations
strucchange Testing, Monitoring, and Dating Structural
Changes
SummarizedExperiment SummarizedExperiment container
tcltk2 Tcl/Tk Additions
TeachingDemos Demonstrations for teaching and learning
tensor Tensor product of arrays
testthat Unit Testing for R
tgp Bayesian treed Gaussian process models
TH.data TH's Data Archive
timeDate Rmetrics - Chronological and Calendar Objects
timeSeries Rmetrics - Financial Time Series Objects
tkrplot TK Rplot
truncnorm Truncated normal distribution
tseries Time Series Analysis and Computational Finance
urca Unit Root and Cointegration Tests for Time
Series Data
VariantAnnotation Annotation of Genetic Variants
vcd Visualizing Categorical Data
vcdExtra 'vcd' Extensions and Additions
vegan Community Ecology Package
VGAM Vector Generalized Linear and Additive Models
vioplot Violin plot
WDI World Development Indicators (World Bank)
XML Tools for Parsing and Generating XML Within R
and S-Plus
XMLRPC Remote Procedure Call (RPC) via XML in R
xtable Export tables to LaTeX or HTML
xts eXtensible Time Series
XVector Representation and manpulation of external
sequences
yaml Methods to convert R data to YAML and back
Zelig Everyone's Statistical Software
zoo S3 Infrastructure for Regular and Irregular
Time Series (Z's Ordered Observations)
Packages in library ‘/usr/lib/R/library’:
base The R Base Package
boot Bootstrap Functions (Originally by Angelo Canty
for S)
class Functions for Classification
cluster "Finding Groups in Data": Cluster Analysis
Extended Rousseeuw et al.
codetools Code Analysis Tools for R
compiler The R Compiler Package
datasets The R Datasets Package
foreign Read Data Stored by Minitab, S, SAS, SPSS,
Stata, Systat, Weka, dBase, ...
graphics The R Graphics Package
grDevices The R Graphics Devices and Support for Colours
and Fonts
grid The Grid Graphics Package
KernSmooth Functions for Kernel Smoothing Supporting Wand
& Jones (1995)
lattice Trellis Graphics for R
MASS Support Functions and Datasets for Venables and
Ripley's MASS
Matrix Sparse and Dense Matrix Classes and Methods
methods Formal Methods and Classes
mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML
Smoothness Estimation
nlme Linear and Nonlinear Mixed Effects Models
nnet Feed-Forward Neural Networks and Multinomial
Log-Linear Models
parallel Support for Parallel computation in R
rpart Recursive Partitioning and Regression Trees
spatial Functions for Kriging and Point Pattern
Analysis
splines Regression Spline Functions and Classes
stats The R Stats Package
stats4 Statistical Functions using S4 Classes
survival Survival Analysis
tcltk Tcl/Tk Interface
tools Tools for Package Development
utils The R Utils Package
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