DRIMSeq

Package: DRIMSeq
Type: Package
Title: Differential splicing and sQTL analyses with
Dirichlet-multinomial model in RNA-Seq
Version: 1.0.2
Date: 2016-03-29
Authors@R: c(person(given = "Malgorzata", family = "Nowicka",
role = c("aut", "cre"),
email = "gosia.nowicka@uzh.ch"))
Description: The package provides two frameworks. One for the differential
splicing analysis between different conditions and one for the sQTL analysis.
Both are based on modeling the counts of genomic features (i.e., transcripts,
exons or exonic bins) with Dirichlet-multinomial distribution. The package also
makes available functions for visualization and exploration of the data and
results.
biocViews: SNP, AlternativeSplicing, DifferentialSplicing, Genetics,
RNASeq, Sequencing, WorkflowStep, MultipleComparison,
GeneExpression, DifferentialExpression
License: GPL (>= 3)
Depends: R (>= 3.3.0)
Imports: GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods,
BiocParallel, edgeR, utils, stats, grDevices, ggplot2, reshape2
Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid,
BiocStyle, knitr, testthat
LazyData: true
ByteCompile: false
VignetteBuilder: knitr
Collate: 'DRIMSeq.R' 'class_show_utils.R' 'class_MatrixList.R'
'class_dmDSdata.R' 'class_dmDSdispersion.R' 'class_dmDSfit.R'
'class_dmDStest.R' 'class_dmSQTLdata.R'
'class_dmSQTLdispersion.R' 'class_dmSQTLfit.R'
'class_dmSQTLtest.R' 'dmDS_adjustmentCommon.R'
'dmDS_estimateCommonDispersion.R'
'dmDS_estimateTagwiseDispersion.R' 'dmDS_filter.R'
'dmDS_fitOneModel.R' 'dmDS_plotFit.R' 'dmDS_profileLikCommon.R'
'dmDS_test.R' 'dmSQTL_adjustmentCommon.R'
'dmSQTL_estimateCommonDispersion.R'
'dmSQTL_estimateTagwiseDispersion.R' 'dmSQTL_filter.R'
'dmSQTL_fitOneModel.R' 'dmSQTL_plotFit.R'
'dmSQTL_profileLikCommon.R' 'dmSQTL_test.R' 'dm_Hessian.R'
'dm_NewtonRaphson.R' 'dm_adjustmentOneGeneManyGroups.R'
'dm_adjustmentOneGeneOneGroup.R' 'dm_colorb.R' 'dm_deviance.R'
'dm_estimateMeanExpression.R' 'dm_fitOneGeneManyGroups.R'
'dm_fitOneGeneOneGroup.R' 'dm_lik.R' 'dm_plotData.R'
'dm_plotDispersion.R' 'dm_plotProportions.R' 'dm_plotPvalues.R'
'dm_profileLikTagwise.R' 'dm_rdirichlet.R' 'dm_score.R'
'dm_weirMoM.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 06:03:39 UTC; biocbuild
Author: Malgorzata Nowicka [aut, cre]
Maintainer: Malgorzata Nowicka <gosia.nowicka@uzh.ch>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'DRIMSeq' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DRIMSeq'
    finding HTML links ... done
    MatrixList-class                        html  
    data_dmDSdata                           html  
    data_dmSQTLdata                         html  
    dmDSdata-class                          html  
    dmDSdata                                html  
    dmDSdispersion-class                    html  
    dmDSfit-class                           html  
    dmDStest-class                          html  
    dmDispersion                            html  
    finding level-2 HTML links ... done

    dmFilter                                html  
    dmFit                                   html  
    dmSQTLdata-class                        html  
    dmSQTLdata                              html  
    dmSQTLdispersion-class                  html  
    dmSQTLfit-class                         html  
    dmSQTLtest-class                        html  
    dmTest                                  html  
    dm_plotDataDSInfo                       html  
    dm_plotProportions                      html  
    plotData                                html  
    plotDispersion                          html  
    plotFit                                 html  
    plotTest                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DRIMSeq)
Making 'packages.html' ... done