abind, covr, doParallel, foreach, iterators, itertools,
tcltk, testthat

Stefan Milton Bache <stefan@stefanbache.dk> and
    Hadley Wickham <h.wickham@gmail.com>

Provides a mechanism for chaining commands with a
    new forward-pipe operator, %>%. This operator will forward a
    value, or the result of an expression, into the next function
    call/expression. There is flexible support for the type
    of right-hand side expressions. For more information, see
    package vignette.
    To quote Rene Magritte, "Ceci n'est pas un pipe."

Encapsulated Classes with Reference Semantics

person("Winston", "Chang", role = c("aut", "cre"), email = "winston@stdout.org")

Creates classes with reference semantics, similar to R's built-in
    reference classes. Compared to reference classes, R6 classes are simpler
    and lighter-weight, and they are not built on S4 classes so they do not
    require the methods package. These classes allow public and private
    members, and they support inheritance, even when the classes are defined in
    different packages.

knitr, microbenchmark, pryr, testthat, ggplot2, scales

Foundation of integer range manipulation in Bioconductor

Provides efficient low-level and highly reusable S4
	classes for storing, manipulating and aggregating over annotated
	ranges of integers. Implements an algebra of range operations,
	including efficient algorithms for finding overlaps and nearest
	neighbors. Defines efficient list-like classes for storing,
	transforming and aggregating large grouped data, i.e., collections
	of atomic vectors and DataFrames.

R (>= 3.1.0), methods, utils, stats, BiocGenerics (>= 0.25.3),
S4Vectors (>= 0.27.12)

XVector, GenomicRanges, Rsamtools, GenomicAlignments,
GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,
RUnit, BiocStyle

range-squeezers.R Vector-class-leftovers.R
DataFrameList-class.R DataFrameList-utils.R AtomicList-class.R
AtomicList-utils.R Ranges-and-RangesList-classes.R
IPosRanges-class.R IPosRanges-comparison.R
IntegerRangesList-class.R IRanges-class.R IRanges-constructor.R
IRanges-utils.R Rle-class-leftovers.R IPos-class.R
subsetting-utils.R Grouping-class.R Views-class.R
RleViews-class.R RleViews-utils.R extractList.R seqapply.R
multisplit.R SimpleGrouping-class.R IRangesList-class.R
IPosList-class.R ViewsList-class.R RleViewsList-class.R
RleViewsList-utils.R RangedSelection-class.R
MaskCollection-class.R read.Mask.R CompressedList-class.R
CompressedList-comparison.R CompressedHitsList-class.R
CompressedDataFrameList-class.R CompressedAtomicList-class.R
CompressedGrouping-class.R CompressedRangesList-class.R
Hits-class-leftovers.R NCList-class.R findOverlaps-methods.R
windows-methods.R intra-range-methods.R inter-range-methods.R
reverse-methods.R coverage-methods.R cvg-methods.R
slice-methods.R setops-methods.R nearest-methods.R
cbind-Rle-methods.R tile-methods.R extractListFragments.R zzz.R