The package implements an algorithm for fast gene set enrichment
    analysis. Using the fast algorithm allows to make more permutations and get
    more fine grained p-values, which allows to use accurate stantard approaches to
    multiple hypothesis correction.

data.table, BiocParallel, stats, ggplot2 (>= 2.2.0),
gridExtra, grid, fastmatch, Matrix, utils

testthat, knitr, rmarkdown, reactome.db, AnnotationDbi,
parallel, org.Mm.eg.db, limma, GEOquery

Gennady Korotkevich [aut],
  Vladimir Sukhov [aut],
  Alexey Sergushichev [aut, cre]

Interface and language bindings to Tcl/Tk GUI elements.

Routines for simple graphs and network analysis. It can
  handle large graphs very well and provides functions for generating random
  and regular graphs, graph visualization, centrality methods and much more.

graphics, grDevices, magrittr, Matrix, pkgconfig (>= 2.0.0),
stats, utils

ape, digest, graph, igraphdata, rgl, scales, stats4, tcltk,
testthat

gmp (optional), libxml2 (optional), glpk (optional)

'adjacency.R' 'auto.R' 'assortativity.R' 'attributes.R'
'basic.R' 'bipartite.R' 'centrality.R' 'centralization.R'
'cliques.R' 'cocitation.R' 'cohesive.blocks.R' 'community.R'
'components.R' 'console.R' 'conversion.R' 'data_frame.R'
'decomposition.R' 'degseq.R' 'demo.R' 'embedding.R' 'epi.R'
'fit.R' 'flow.R' 'foreign.R' 'games.R' 'glet.R' 'hrg.R'
'igraph-package.R' 'incidence.R' 'indexing.R' 'interface.R'
'iterators.R' 'layout.R' 'layout_drl.R' 'lazyeval.R' 'make.R'
'minimum.spanning.tree.R' 'motifs.R' 'nexus.R' 'operators.R'
'other.R' 'package.R' 'palette.R' 'par.R' 'paths.R' 'plot.R'
'plot.common.R' 'plot.shapes.R' 'pp.R' 'print.R' 'printr.R'
'random_walk.R' 'rewire.R' 'scan.R' 'scg.R' 'sgm.R'
'similarity.R' 'simple.R' 'sir.R' 'socnet.R' 'sparsedf.R'
'structural.properties.R' 'structure.info.R' 'test.R'
'tkplot.R' 'topology.R' 'triangles.R' 'utils.R' 'uuid.R'
'versions.R' 'weakref.R' 'zzz-deprecate.R'

Exploratory analysis for two-color spotted microarray data

Yee Hwa (Jean) Yang <jeany@maths.usyd.edu.au> with contributions
        from Agnes Paquet and Sandrine Dudoit.