Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>=
2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>=
1.13.53), GenomicAlignments, rtracklayer, BSgenome,
GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub,
DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14,
pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe,
BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Athaliana.BioMart.plantsmart22,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr,
rmarkdown, BiocStyle

normarg-utils.R utils.R phicoef.R transcript-utils.R
constraint.R strand-utils.R genomic-range-squeezers.R
GenomicRanges-class.R GenomicRanges-comparison.R
GRanges-class.R GPos-class.R GRangesFactor-class.R
DelegatingGenomicRanges-class.R GNCList-class.R
GenomicRangesList-class.R GRangesList-class.R
makeGRangesFromDataFrame.R makeGRangesListFromDataFrame.R
RangedData-methods.R findOverlaps-methods.R
intra-range-methods.R inter-range-methods.R coverage-methods.R
setops-methods.R subtract-methods.R nearest-methods.R
absoluteRanges.R tileGenome.R tile-methods.R genomicvars.R
zzz.R

Patrick Aboyoun [aut],
  Hervé Pagès [aut, cre],
  Michael Lawrence [aut],
  Sonali Arora [ctb],
  Martin Morgan [ctb],
  Kayla Morrell [ctb],
  Valerie Obenchain [ctb],
  Marcel Ramos [ctb],
  Lori Shepherd [ctb],
  Dan Tenenbaum [ctb],
  Daniel van Twisk [ctb]

Utilities for manipulating chromosome names, including modifying
them to follow a particular naming style

Contains data and functions that
	define and allow translation between different chromosome
	sequence naming conventions (e.g., "chr1" versus "1"),
	including a function that attempts to place sequence names in
	their natural, rather than lexicographic, order.

c(
	person("Sonali", "Arora", role="aut"),
	person("Martin", "Morgan", role="aut"),
	person("Marc", "Carlson", role="aut"),
	person("Hervé", "Pagès", role=c("aut", "cre"),
		email="hpages.on.github@gmail.com"),
	person("Prisca Chidimma", "Maduka", role="ctb"),
	person("Atuhurira Kirabo", "Kakopo", role="ctb"),
	person("Haleema", "Khan", role="ctb",
		comment="vignette translation from Sweave to Rmarkdown / HTML"),
	person("Emmanuel Chigozie", "Elendu", role="ctb"))