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

Various R Programming Tools for Plotting Data

Various R programming tools for plotting data, including:
  - calculating and plotting locally smoothed summary function as
    ('bandplot', 'wapply'),
  - enhanced versions of standard plots ('barplot2', 'boxplot2',
    'heatmap.2', 'smartlegend'),
  - manipulating colors ('col2hex', 'colorpanel', 'redgreen',
    'greenred', 'bluered', 'redblue', 'rich.colors'),
  - calculating and plotting two-dimensional data summaries ('ci2d',
    'hist2d'),
  - enhanced regression diagnostic plots ('lmplot2', 'residplot'),
  - formula-enabled interface to 'stats::lowess' function ('lowess'),
  - displaying textual data in plots ('textplot', 'sinkplot'),
  - plotting a matrix where each cell contains a dot whose size
    reflects the relative magnitude of the elements ('balloonplot'),
  - plotting "Venn" diagrams ('venn'),
  - displaying Open-Office style plots ('ooplot'),
  - plotting multiple data on same region, with separate axes
    ('overplot'),
  - plotting means and confidence intervals ('plotCI', 'plotmeans'),
  - spacing points in an x-y plot so they don't overlap ('space').