The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Software for Computing and Annotating Genomic Ranges
Open accessAbstract
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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Cites
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
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Allen, J. F. (1983) · Communications of the ACM · doi:10.1145/182.358434 · Cited by 7,593 · cited 1×
“The algorithm supports several types of overlap, including those defined by Allen’s Interval Algebra [5].”
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Wu, T. D., & Nacu, S. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq057 · Cited by 1,894
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Cited by
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106
Self-citationHTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464
Self-citationMaftools: efficient and comprehensive analysis of somatic variants in cancer
Mayakonda, A., Lin, D.-C., Assenov, Y., Plass, C., & Koeffler, H. P. (2018) · Genome Research · doi:10.1101/gr.239244.118 · Cited by 4,935
Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
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Genomic atlas of the human plasma proteome
Sun, B. B., Maranville, J. C., Peters, J. E., Stacey, D., Staley, J. R., Blackshaw, J., Burgess, S., Jiang, T., Paige, E., Surendran, P., et al. (2018) · Nature · doi:10.1038/s41586-018-0175-2 · Cited by 2,268
Metadata
- Authors
- Lawrence, M., Huber, W., Pagès, H., Aboyoun, P., Carlson, M., Gentleman, R., Morgan, M. T., & Carey, V. J.
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-08-08
- Volume
- 9
- Issue
- 8
- Pages
- e1003118
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W2131478115
- Cited by
- 4,398
- References
- 3
- FWCI
- 36.31
- Type
- journal article
- Language
- en
- Open access
- gold
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- Lawrence, M., Huber, W., Pagès, H., Aboyoun, P., Carlson, M., Gentleman, R., Morgan, M. T., & Carey, V. J. (2013). Software for Computing and Annotating Genomic Ranges. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1003118
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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