metagenomeSeq

Package: metagenomeSeq
Title: Statistical analysis for sparse high-throughput sequencing
Version: 1.14.2
Date: 2016-04-17
Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
Bravo
Maintainer: Joseph N. Paulson <jpaulson@jimmy.harvard.edu>
Description: metagenomeSeq is designed to determine features (be it
Operational Taxanomic Unit (OTU), species, etc.) that are
differentially abundant between two or more groups of multiple
samples. metagenomeSeq is designed to address the effects of
both normalization and under-sampling of microbial communities
on disease association detection and the testing of feature
correlations.
License: Artistic-2.0
Depends: R (>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer
Suggests: annotate, BiocGenerics, biomformat, knitr, gss, RUnit, vegan,
interactiveDisplay
Imports: parallel, matrixStats, foreach, Matrix, gplots
VignetteBuilder: knitr
URL: https://github.com/nosson/metagenomeSeq/
BugReports: https://github.com/nosson/metagenomeSeq/issues
biocViews: Classification, Clustering, GeneticVariability,
DifferentialExpression, Microbiome, Metagenomics,
Normalization, Visualization, MultipleComparison, Sequencing,
Software
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 03:51:39 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'metagenomeSeq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'metagenomeSeq'
    finding HTML links ... done
    MRcoefs                                 html  
    MRcounts                                html  
    MRexperiment-class                      html  
    MRexperiment2biom                       html  
    MRfulltable                             html  
    MRtable                                 html  
    aggregateBySample                       html  
    aggregateByTaxonomy                     html  
    biom2MRexperiment                       html  
    calcNormFactors                         html  
    calcPosComponent                        html  
    calcShrinkParameters                    html  
    calcStandardError                       html  
    calcZeroAdjustment                      html  
    calcZeroComponent                       html  
    calculateEffectiveSamples               html  
    correctIndices                          html  
    correlationTest                         html  
    cumNorm                                 html  
    cumNormMat                              html  
    cumNormStat                             html  
    cumNormStatFast                         html  
    doCountMStep                            html  
    doEStep                                 html  
    doZeroMStep                             html  
    expSummary                              html  
    exportMat                               html  
    exportStats                             html  
    filterData                              html  
    fitDO                                   html  
    fitFeatureModel                         html  
    fitLogNormal                            html  
    fitPA                                   html  
    fitSSTimeSeries                         html  
    fitTimeSeries                           html  
    fitZeroLogNormal                        html  
    fitZig                                  html  
    getCountDensity                         html  
    getEpsilon                              html  
    getNegativeLogLikelihoods               html  
    getPi                                   html  
    getZ                                    html  
    isItStillActive                         html  
    libSize                                 html  
    load_biom                               html  
    load_meta                               html  
    load_metaQ                              html  
    load_phenoData                          html  
    lungData                                html  
    makeLabels                              html  
    metagenomeSeq-deprecated                html  
    metagenomeSeq-package                   html  
    mouseData                               html  
    newMRexperiment                         html  
    normFactors                             html  
    plotBubble                              html  
    plotClassTimeSeries                     html  
    plotCorr                                html  
    plotFeature                             html  
    plotGenus                               html  
    plotMRheatmap                           html  
    plotOTU                                 html  
    plotOrd                                 html  
    plotRare                                html  
    plotTimeSeries                          html  
    posteriorProbs                          html  
    returnAppropriateObj                    html  
    ssFit                                   html  
    ssIntervalCandidate                     html  
    ssPerm                                  html  
    ssPermAnalysis                          html  
    trapz                                   html  
    uniqueFeatures                          html  
    zigControl                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metagenomeSeq)
Making 'packages.html' ... done