monocle

Package: monocle
Type: Package
Title: Analysis tools for single-cell expression experiments.
Version: 1.6.2
Date: 2013-11-19
Author: Cole Trapnell
Maintainer: Cole Trapnell <coletrap@uw.edu>
Description: Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.
License: Artistic-2.0
Depends: R (>= 2.7.0), HSMMSingleCell (>= 0.101.5), Biobase, ggplot2 (>=
0.9.3.1), splines, VGAM (>= 0.9-5), igraph (>= 0.7.0), plyr
Imports: BiocGenerics, cluster, combinat, fastICA, grid, irlba,
matrixStats, methods, parallel, reshape2, stats, utils, limma
VignetteBuilder: knitr
Suggests: knitr, Hmisc
Roxygen: list(wrap = FALSE)
LazyData: true
biocViews: Sequencing, RNASeq, GeneExpression, DifferentialExpression,
Infrastructure, DataImport, DataRepresentation, Visualization,
Clustering, MultipleComparison, QualityControl
Packaged: 2016-05-16 04:33:27 UTC; biocbuild
NeedsCompilation: no

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'monocle' ...
** R
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: as.vector, unlist
** help
*** installing help indices
  converting help for package 'monocle'
    finding HTML links ... done
    CellDataSet                             html  
    cellPairwiseDistances-set               html  
    cellPairwiseDistances                   html  
    clusterGenes                            html  
    compareModels                           html  
    detectGenes                             html  
    differentialGeneTest                    html  
    fitModel                                html  
    minSpanningTree-set                     html  
    minSpanningTree                         html  
    newCellDataSet                          html  
    orderCells                              html  
    plot_clusters                           html  
    plot_genes_in_pseudotime                html  
    plot_genes_jitter                       html  
    plot_genes_positive_cells               html  
    plot_spanning_tree                      html  
    reduceDimension                         html  
    reducedDimA-set                         html  
    reducedDimA                             html  
    reducedDimS-set                         html  
    reducedDimS                             html  
    reducedDimW-set                         html  
    reducedDimW                             html  
    responseMatrix                          html  
    selectNegentropyGenes                   html  
    setOrderingFilter                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: as.vector, unlist
* DONE (monocle)
Making 'packages.html' ... done