Software for computing and annotating genomic ranges
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 pa...
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Published in | PLoS computational biology Vol. 9; no. 8; p. e1003118 |
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Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
Published |
United States
Public Library of Science
01.08.2013
Public Library of Science (PLoS) |
Subjects | |
Online Access | Get full text |
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Summary: | 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. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Analyzed the data: ML VJC. Contributed reagents/materials/analysis tools: ML HP PA MC MTM. Wrote the paper: ML WH RG MTM VJC. The authors have declared that no competing interests exist. |
ISSN: | 1553-7358 1553-734X 1553-7358 |
DOI: | 10.1371/journal.pcbi.1003118 |