InPAS

Package: InPAS
Type: Package
Title: Identification of Novel alternative PolyAdenylation Sites (PAS)
Version: 1.4.4
Date: 2016-06-20
Authors@R: c(person("Jianhong Ou", "Developer", role = c("aut", "cre"),
email = "jianhong.ou@umassmed.edu"), person("Lihua Julie Zhu",
"Developer", role = "aut", email = "Julie.Zhu@umassmed.edu"))
Author: Jianhong Ou, Sung Mi Park, Michael R. Green and Lihua Julie Zhu
Maintainer: Jianhong Ou <jianhong.ou@umassmed.edu>
Description: Alternative polyadenylation (APA) is one of the important
post-transcriptional regulation mechanisms which occurs in
most human genes. InPAS facilitates the discovery of novel
APA sites from RNAseq data. It leverages cleanUpdTSeq to fine
tune identified APA sites.
biocViews: RNASeq, Sequencing, AlternativeSplicing, Coverage,
DifferentialSplicing, GeneRegulation, Transcription
License: GPL (>= 2)
Lazyload: yes
Imports: AnnotationDbi, BSgenome, cleanUpdTSeq, Gviz, seqinr,
preprocessCore, IRanges, GenomeInfoDb, depmixS4, limma,
BiocParallel
Depends: R (>= 3.1), methods, Biobase, GenomicRanges, GenomicFeatures,
S4Vectors
Suggests: RUnit, BiocGenerics, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10, org.Hs.eg.db, org.Mm.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, rtracklayer, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-21 05:10:44 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'InPAS' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'InPAS'
    finding HTML links ... done
    CPsite_estimation                       html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/CPsite_estimation.Rd:73: missing file link 'BSgenome'
    CPsites                                 html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/CPsites.Rd:26: missing file link 'BSgenome'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/CPsites.Rd:37: missing file link 'cleanUpdTSeq'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/CPsites.Rd:45: missing file link 'TxDb'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/CPsites.Rd:53: missing file link 'PASclassifier'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/CPsites.Rd:61: missing file link 'BiocParallelParam'
    InPAS-package                           html  
    PAscore                                 html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/PAscore.Rd:30: missing file link 'BSgenome'
    PAscore2                                html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/PAscore2.Rd:30: missing file link 'BSgenome'
    UTR3TotalCoverage                       html  
    UTR3eSet                                html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/UTR3eSet.Rd:20: missing file link 'GRanges'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/UTR3eSet.Rd:38: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/UTR3eSet.Rd:39: missing file link 'GRanges'
    UTR3usage                               html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/UTR3usage.Rd:25: missing file link 'BiocParallelParam'
    covThreshold                            html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/covThreshold.Rd:19: missing file link 'BSgenome'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/covThreshold.Rd:22: missing file link 'TxDb'
    coverageFromBedGraph                    html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/coverageFromBedGraph.Rd:21: missing file link 'BiocParallelParam'
    depthWeight                             html  
    distalAdj                               html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/distalAdj.Rd:27: missing file link 'BSgenome'
    filterRes                               html  
    fisher.exact.test                       html  
    get.regions.coverage                    html  
    getCov                                  html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/getCov.Rd:17: missing file link 'BSgenome'
    getUTR3eSet                             html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/getUTR3eSet.Rd:25: missing file link 'BSgenome'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/getUTR3eSet.Rd:37: missing file link 'BiocParallelParam'
    getUTR3region                           html  
    inPAS                                   html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/inPAS.Rd:45: missing file link 'BSgenome'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/inPAS.Rd:47: missing file link 'TxDb'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/inPAS.Rd:79: missing file link 'cleanUpdTSeq'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/inPAS.Rd:82: missing file link 'PASclassifier'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/inPAS.Rd:110: missing file link 'topTable'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/inPAS.Rd:123: missing file link 'BiocParallelParam'
    lastCDSusage                            html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/lastCDSusage.Rd:23: missing file link 'BiocParallelParam'
    limmaAnalyze                            html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/limmaAnalyze.Rd:22: missing file link 'topTable'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/limmaAnalyze.Rd:27: missing file link 'eBayes'
    optimalSegmentation                     html  
    polishCPs                               html  
    prepare4GSEA                            html  
    proximalAdj                             html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/proximalAdj.Rd:25: missing file link 'BSgenome'
    proximalAdjByCleanUpdTSeq               html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/proximalAdjByCleanUpdTSeq.Rd:32: missing file link 'BSgenome'
    proximalAdjByPWM                        html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/proximalAdjByPWM.Rd:32: missing file link 'BSgenome'
    removeUTR3__UTR3                        html  
    searchDistalCPs                         html  
    searchProximalCPs                       html  
    seqLen                                  html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/seqLen.Rd:14: missing file link 'BSgenome'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/seqLen.Rd:24: missing file link 'seqlengths'
    singleGroupAnalyze                      html  
    singleSampleAnalyze                     html  
    finding level-2 HTML links ... done

    sortGR                                  html  
    testUsage                               html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/testUsage.Rd:22: missing file link 'BSgenome'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/testUsage.Rd:25: missing file link 'BiocParallelParam'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/testUsage.Rd:43: missing file link 'topTable'
    totalCoverage                           html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/totalCoverage.Rd:18: missing file link 'BSgenome'
    trimSeqnames                            html  
    usage4plot                              html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/usage4plot.Rd:19: missing file link 'BSgenome'
    utr3.hg19                               html  
    utr3.mm10                               html  
    utr3Annotation                          html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/utr3Annotation.Rd:4: missing file link 'TxDb'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/utr3Annotation.Rd:7: missing file link 'TxDb'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/utr3Annotation.Rd:15: missing file link 'TxDb'
    utr3UsageEstimation                     html  
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/utr3UsageEstimation.Rd:23: missing file link 'BSgenome'
Rd warning: /tmp/RtmpdHObvz/R.INSTALL6ae1184782/InPAS/man/utr3UsageEstimation.Rd:36: missing file link 'BiocParallelParam'
    valley                                  html  
    zScoreThrethold                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (InPAS)
Making 'packages.html' ... done