We describe Bioconductor infrastructure for representing and computing
on annotated genomic ranges and integrating genomic data with the
statistical computing features of R and its extensions. At the core
of the infrastructure are three packages: IRanges, GenomicRanges,
and GenomicFeatures. These packages provide scalable data structures
for representing annotated ranges on the genome, with special support
for transcript structures, read alignments and coverage vectors.
Computational facilities include efficient algorithms for overlap
and nearest neighbor detection, coverage calculation and other range
operations. This infrastructure directly supports more than 80 other
Bioconductor packages, including those for sequence analysis, differential
expression analysis and visualization.
%0 Journal Article
%1 Lawrence2013Softwarecomputingand
%A Lawrence, Michael
%A Huber, Wolfgang
%A Pag�s, Herv�
%A Aboyoun, Patrick
%A Carlson, Marc
%A Gentleman, Robert
%A Morgan, Martin T
%A Carey, Vincent J
%D 2013
%J PLoS Comput Biol
%K imported
%N 8
%P e1003118
%R 10.1371/journal.pcbi.1003118
%T Software for computing and annotating genomic ranges.
%U http://dx.doi.org/10.1371/journal.pcbi.1003118
%V 9
%X We describe Bioconductor infrastructure for representing and computing
on annotated genomic ranges and integrating genomic data with the
statistical computing features of R and its extensions. At the core
of the infrastructure are three packages: IRanges, GenomicRanges,
and GenomicFeatures. These packages provide scalable data structures
for representing annotated ranges on the genome, with special support
for transcript structures, read alignments and coverage vectors.
Computational facilities include efficient algorithms for overlap
and nearest neighbor detection, coverage calculation and other range
operations. This infrastructure directly supports more than 80 other
Bioconductor packages, including those for sequence analysis, differential
expression analysis and visualization.
@article{Lawrence2013Softwarecomputingand,
abstract = {We describe Bioconductor infrastructure for representing and computing
on annotated genomic ranges and integrating genomic data with the
statistical computing features of R and its extensions. At the core
of the infrastructure are three packages: IRanges, GenomicRanges,
and GenomicFeatures. These packages provide scalable data structures
for representing annotated ranges on the genome, with special support
for transcript structures, read alignments and coverage vectors.
Computational facilities include efficient algorithms for overlap
and nearest neighbor detection, coverage calculation and other range
operations. This infrastructure directly supports more than 80 other
Bioconductor packages, including those for sequence analysis, differential
expression analysis and visualization.},
added-at = {2014-05-13T15:48:44.000+0200},
author = {Lawrence, Michael and Huber, Wolfgang and Pag�s, Herv� and Aboyoun, Patrick and Carlson, Marc and Gentleman, Robert and Morgan, Martin T and Carey, Vincent J},
biburl = {https://www.bibsonomy.org/bibtex/288ca707eeed55b9f6c7b4f2b47d3c730/gwotto},
doi = {10.1371/journal.pcbi.1003118},
file = {:Lawrence2013Softwarecomputingand.pdf:PDF},
institution = {Bioinformatics and Computational Biology, Genentech, Inc., South
San Francisco, California, United States of America.},
interhash = {0a03a98aac2a56cb205f8b65e9c46c4e},
intrahash = {88ca707eeed55b9f6c7b4f2b47d3c730},
journal = {PLoS Comput Biol},
keywords = {imported},
language = {eng},
medline-pst = {ppublish},
month = Aug,
number = 8,
owner = {gotto},
pages = {e1003118},
pii = {PCOMPBIOL-D-13-00147},
pmid = {23950696},
timestamp = {2014-05-13T15:48:44.000+0200},
title = {Software for computing and annotating genomic ranges.},
url = {http://dx.doi.org/10.1371/journal.pcbi.1003118},
volume = 9,
year = 2013
}