Chromosome name
Base pair start position
Base pair end position
Percentage of non-N nucleotides (of full bin size)
Percentage of C and G nucleotides (of non-N nucleotides)
Average mappability of 50mers with a maximum of 2 mismatches
Percent overlap with ENCODE blacklisted regions
Median loess residual from 1000 Genomes (50mers)
Whether the bin should be used in subsequent analysis steps

Quantitative DNA sequencing for chromosomal aberrations

c(person("Ilari", "Scheinin", role=c("aut", "cre", "cph"),
  email = "firstname.lastname@gmail.com"))

Quantitative DNA sequencing for chromosomal aberrations.

Homo sapiens (Human) full genome (UCSC version hg19)

Homo sapiens (Human) full genome as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects.

Infrastructure for Biostrings-based genome data packages

Infrastructure shared by all the Biostrings-based genome data
             packages

Genetics, Infrastructure, DataRepresentation,
SequenceMatching, Annotation, SNP

methods, BiocGenerics, IRanges, GenomicRanges, Biostrings

RUnit, BSgenome.Celegans.UCSC.ce2 (>= 1.3.11),
BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.11),
SNPlocs.Hsapiens.dbSNP.20100427, hgu95av2probe, Biobase

utils.R available.genomes.R GenomeDescription-class.R
SNPlocs-class.R InjectSNPsHandler-class.R BSgenome-class.R
injectSNPs.R getSeq-methods.R bsapply.R BSgenome-utils.R
GenomeData-class.R GenomeDataList-class.R gdapply.R gdReduce.R
BSgenomeForge.R

String objects representing biological sequences, and matching
algorithms

Memory efficient string containers, string matching
	algorithms, and other utilities, for fast manipulation of large
	biological sequences or sets of sequences.

H. Pages, P. Aboyoun, R. Gentleman, and S. DebRoy

SequenceMatching, Genetics, Sequencing, Infrastructure,
DataImport, DataRepresentation

graphics, methods, stats, utils, BiocGenerics, IRanges,
XVector

BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=
1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),
BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,
hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy,
affydata (>= 1.11.5), RUnit