cellTree

Package: cellTree
Title: Inference and visualisation of Single-Cell RNA-seq data as a
hierarchical tree structure
Version: 1.2.2
Authors@R: c(person("David", "duVerle", email = "dave@cb.k.u-tokyo.ac.jp", role = c("aut",
"cre")), person("Koji", "Tsuda", email = "tsuda@k.u-tokyo.ac.jp", role = c("aut")))
Authors: David duVerle [aut, cre], Koji Tsuda [aut]
Encoding: UTF-8
Description: This packages computes a Latent Dirichlet Allocation (LDA) model of single-cell
RNA-seq data and builds a compact tree modelling the relationship between
individual cells over time or space.
Depends: R (>= 3.3), topGO
License: Artistic-2.0
LazyData: true
RoxygenNote: 5.0.1
VignetteBuilder: knitr
URL: http://tsudalab.org
Imports: topicmodels, slam, maptpx, igraph, xtable, gplots
Suggests: BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db,
Biobase, tools
biocViews: Sequencing, RNASeq, Clustering, GraphAndNetwork,
Visualization, GeneExpression, GeneSetEnrichment,
BiomedicalInformatics, CellBiology, FunctionalGenomics,
SystemsBiology, GO, TimeCourse, Microarray
NeedsCompilation: no
Author: David duVerle [aut, cre], Koji Tsuda [aut]
Maintainer: David duVerle <dave@cb.k.u-tokyo.ac.jp>
Packaged: 2016-05-16 05:56:07 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'cellTree' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
  converting help for package 'cellTree'
    finding HTML links ... done
    HSMM_lda_model                          html  
    cell.ordering.table                     html  
Rd warning: /tmp/RtmpjBgk2U/R.INSTALLfb35a9cd3b3/cellTree/man/cell.ordering.table.Rd:10: missing file link 'igraph'
    cellTree-package                        html  
    compute.backbone.tree                   html  
Rd warning: /tmp/RtmpjBgk2U/R.INSTALLfb35a9cd3b3/cellTree/man/compute.backbone.tree.Rd:34: missing file link 'igraph'
    compute.go.enrichment                   html  
Rd warning: /tmp/RtmpjBgk2U/R.INSTALLfb35a9cd3b3/cellTree/man/compute.go.enrichment.Rd:30: missing file link 'igraph'
    compute.lda                             html  
Rd warning: /tmp/RtmpjBgk2U/R.INSTALLfb35a9cd3b3/cellTree/man/compute.lda.Rd:25: missing file link 'LDA-class'
Rd warning: /tmp/RtmpjBgk2U/R.INSTALLfb35a9cd3b3/cellTree/man/compute.lda.Rd:69: missing file link 'LDA'
Rd warning: /tmp/RtmpjBgk2U/R.INSTALLfb35a9cd3b3/cellTree/man/compute.lda.Rd:69: missing file link 'LDA_Gibbscontrol-class'
Rd warning: /tmp/RtmpjBgk2U/R.INSTALLfb35a9cd3b3/cellTree/man/compute.lda.Rd:69: missing file link 'CTM_VEMcontrol-class'
    ct.plot.go.dag                          html  
Rd warning: /tmp/RtmpjBgk2U/R.INSTALLfb35a9cd3b3/cellTree/man/ct.plot.go.dag.Rd:27: missing file link 'igraph'
    ct.plot.grouping                        html  
Rd warning: /tmp/RtmpjBgk2U/R.INSTALLfb35a9cd3b3/cellTree/man/ct.plot.grouping.Rd:12: missing file link 'igraph'
Rd warning: /tmp/RtmpjBgk2U/R.INSTALLfb35a9cd3b3/cellTree/man/ct.plot.grouping.Rd:31: missing file link 'igraph'
    ct.plot.heatmap                         html  
    ct.plot.topics                          html  
Rd warning: /tmp/RtmpjBgk2U/R.INSTALLfb35a9cd3b3/cellTree/man/ct.plot.topics.Rd:12: missing file link 'igraph'
Rd warning: /tmp/RtmpjBgk2U/R.INSTALLfb35a9cd3b3/cellTree/man/ct.plot.topics.Rd:27: missing file link 'igraph'
    get.cell.dists                          html  
    go.results.to.latex                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (cellTree)
Making 'packages.html' ... done