Software for Computing and Annotating Genomic Ranges

PLoS Computational Biology

Volumn 9, Issue 8, 2013, Pages

  Lawrence, Michael ^a   Huber, Wolfgang ^b,c   Pagès, Hervé ^d   Aboyoun, Patrick ^d   Carlson, Marc ^d   Gentleman, Robert ^a   Morgan, Martin T ^d   Carey, Vincent J ^e  

^a GENENTECH INC   (United States)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^d Fred Hutchinson Cancer Research Center   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL EFFICIENCY; GENES;

BIOCONDUCTORS; DETECTION COVERAGE; EXPRESSION ANALYSIS; EXPRESSION VISUALIZATION; GENOMIC DATA; GENOMICS; NEAREST-NEIGHBOUR; NEIGHBOR DETECTIONS; SEQUENCE ANALYSIS; STATISTICAL COMPUTING;

GENOME;

ARTICLE; BIOINFORMATICS; BIOSENSOR; COMPUTER ANALYSIS; COMPUTER MODEL; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; GENE EXPRESSION; GENETIC ALGORITHM; GENOME ANALYSIS; GENOMICS; K NEAREST NEIGHBOR; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; PROCESS DESIGN; PROCESS DEVELOPMENT; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SYSTEM ANALYSIS;

EID: 84883368195     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003118     Document Type: Article

References (15)

1. Gentleman RC, Carey VJ, Bates DM, et al. (2004) Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology 5: R80.
2. Quinlan AR, Hall IM, (2010) BEDTools: a exible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
3. Ji H, Jiang H, Ma W, Johnson DS, Myers RM, et al. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nature Biotechnology 26: 1293-1300.
4. Cormen TH, Leiserson CE, Rivest RL, Stein C (2001) Introduction to algorithms. Cambridge, Mass: MIT Press.
5. Allen JF, (1983) Maintaining knowledge about temporal intervals. Communications of the ACM 26: 832-843.
6. Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18: 1851-8.
7. Morgan M, Anders S, Lawrence M, Aboyoun P, Pagues H, et al. (2009) ShortRead: a Bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics 25: 2607-2608.
8. Sarkar D, Gentleman R, Lawrence M, Yao Z (2013) chipseq: A package for analyzing ChIP-seq data. R package version 1.10.1. Available: http://www.bioconductor.org/packages/2.12/bioc/html/chipseq.html.
9. Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G, (2008) Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not con-served across closely related yeast species. PLoS Genet 4: e1000299.
10. McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, et al. (2010) Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328: 235-9.
11. Wu TD, Nacu S, (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics (Oxford, England) 26: 873-81.
12. Lawrence M, Gentleman R, Carey V, (2009) rtracklayer: an R package for interfacing with genome browsers. Bioinformatics 25: 1841-1842.
13. Morgan M, Pages H (2013) Rsamtools: Binary alignment (BAM), variant call (BCF), or tabix file import. R package version 1.12.3. Available: http://www.bioconductor.org/packages/2.12/bioc/html/Rsamtools.html.
14. Pagès H, Aboyoun P, Gentleman R, DebRoy S (2013) Biostrings: String objects representing biological sequences, and matching algorithms. R package version 2.28.0. Available: http://www.bioconductor.org/packages/2.12/bioc/html/Biostrings.html.
15. Lawrence M, Degenhardt J, Gentleman R (2013) Variant-Tools: Tools for Working with Genetic Variants. R package version 1.2.2. Available: http://www.bioconductor.org/packages/2.12/bioc/html/VariantTools.html.