GenomicRanges pipeline

GenomicRanges specifications

Information


Unique identifier OMICS_01161
Name GenomicRanges
Alternative name GenomicAlignments
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.30.0
Stability Stable
Requirements methods, stats4, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb
Maintained Yes

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Maintainer


  • person_outline Michael Lawrence <>

Publication for GenomicRanges

GenomicRanges IN pipelines

 (8)
2018
PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] the following line to extract gzipped file #gunzip("hg19tohg38.over.chain.gz") ch <- import.chain("hg19tohg38.over.chain") gtex_blood <- unlist(liftover(gtex_blood, ch)) , we will use the genomicranges package 45 to compute the overlap between gwas snps and blood eqtls:, library (genomicranges) hits <- findoverlaps(snps_hard, gtex_blood) snps_hard_in_gtex_blood = […]

2018
PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] gtex_blood <- unlist(liftover(gtex_blood, ch)) , we will use the genomicranges package 45 to compute the overlap between gwas snps and blood eqtls:, library (genomicranges) hits <- findoverlaps(snps_hard, gtex_blood) snps_hard_in_gtex_blood = snps_hard[queryhits(hits)] gtex_blood_with_snps_hard = gtex_blood[subjecthits(hits)] […]

2018
PMCID: 5923265
PMID: 29703886
DOI: 10.1038/s41467-018-04125-8

[…] mapped to the mm9 genome using tophat261 and the ucsc mm9 known gene reference transcript database62. for each sample, reads that overlapped exons of unique entrez genes were annotated using the genomicranges (v1.22.4) package in r/bioconductor. genes with less than 3 reads per million in at least 3 samples were removed and edger63 used to find significantly differentially expressed genes […]

2017
PMCID: 5645312
PMID: 29042584
DOI: 10.1038/s41598-017-13731-3

[…] and normalized as described by dixon et al.8., all of the computations were performed using ipython 5.0, r version 3.2.2 and the bioconductor (3.3), qvalue (3.2.3), limma (3.2.4), diptest (3.2.0), genomicranges (3.2.3), edger (3.2.0), and genefilter (3.2.3). all of the figures were made using basic r graphics and packages gplots (3.2.4), and vioplot (3.2.0). all scripts used here are available […]

2016
PMCID: 4904357
PMID: 27291689
DOI: 10.1186/s12916-016-0632-4

[…] [46]. the command line utility picard was used to sort the resulting bam alignment files [47]. samples were quality assessed using fastqc [48]. gene level read counts were generated in r using the genomicranges and rsamtools bioconductor packages against the mus musculus gtf annotation file version grcm38 (release 73)[49–51]. a total of 269 gigabytes of sequencing data from 57 samples […]

GenomicRanges institution(s)
Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA; European Molecular Biology Laboratory Genome Biology Unit, Heidelberg, Germany; The European Bioinformatics Institute, Cambridge, UK; Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
GenomicRanges funding source(s)
Supported by the National Institutes of Health, National Human Genome Research Group through grants P41 HG004059 and U41 HG004059 and by National Heart, Lung and Blood Institute grants R01 HL086601, R01 HL093076 and R01 HL094635.

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