GenomicRanges protocols

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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 1.32.7
Stability Stable
Requirements
methods, stats, KEGG.db, Biobase, Matrix, utils, rtracklayer, BiocStyle, stats4, GenomicAlignments, edgeR, DESeq2, BSgenome, BSgenome.Hsapiens.UCSC.hg19, Gviz, R(>=2.10), RUnit, GenomicFeatures, org.Hs.eg.db, annotate, BSgenome.Mmusculus.UCSC.mm10, org.Mm.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocGenerics(>=0.25.3), S4Vectors(>=0.17.32), IRanges(>=2.14.4), GenomeInfoDb(>=1.15.2), XVector(>=0.19.8), AnnotationDbi(>=1.21.1), Biostrings(>=2.25.3), Rsamtools(>=1.13.53), SummarizedExperiment(>=0.1.5), VariantAnnotation, AnnotationHub, DEXSeq, KEGGgraph, digest, BSgenome.Scerevisiae.UCSC.sacCer2, hgu95av2.db, org.Sc.sgd.db, pasilla, pasillaBamSubset, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RNAseqData.HNRNPC.bam.chr14, hgu95av2probe
Maintained Yes

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  • person_outline Michael Lawrence <>

Publication for GenomicRanges

GenomicRanges in pipelines

 (36)
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 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: 5908308
PMID: 29682207
DOI: 10.18632/oncotarget.24907

[…] respectively., for defining scna groups, we performed pam using the copy number segment mean called per sample in each region that passed fdr q<0.15. overlap of each region was performed using genomicranges. for caucasians, we selected a pam cluster solution of five; for boaas, we selected four. clustering and heatmap generation was performed using the complexheatmap package []. […]

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

[…] were mapped to the mm9 genome using tophat2 and the ucsc mm9 known gene reference transcript database. 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 edger used to find significantly differentially expressed genes […]

2017
PMCID: 5325622
PMID: 28112643
DOI: 10.7554/eLife.21883.061

[…] () and rcolorbrewer () for heatmap color selection; dendextend for plotting dendrograms (); gviz for plots of chromosome ideograms (); upsetr for plotting overlaps between sets of atac-seq peaks (); genomicranges for calculations involving peak and tss positions in the genome (); rtracklayer () for access to refseq data from the ucsc genome browser database; genomicalignments for manipulating […]

2017
PMCID: 5332558
PMID: 28215706
DOI: 10.1016/j.cell.2017.01.019

[…] genome assembly using bwa v0.5.9 and v0.7.10 () respectively with default settings. bam files were sorted and indexed using samtools (). further analysis was conducted using bioconductor and its genomicranges package (). reads were extended to 250 bp and each sample was normalized to a read depth of 20 million., a subset of the protein coding human ensembl transcriptome was created […]


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GenomicRanges in publications

 (184)
PMCID: 5953949
PMID: 29765016
DOI: 10.1038/s41467-018-04234-4

[…] ). accessible regions were determined using macs2 (v2.1.0.20151222) with the following options: “callpeak -g mm –q 0.01”. the union of all sample peaks was determined in r (v3.2.3) using the package “genomicranges” (v1.22.4). the number of reads in accessible regions was used to normalize the signal with the following equation:1\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage […]

PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] this procedure were controlled manually using the integrative genomics viewer (igv)., sashimi plots were generated with the r software version 3.4.2 and its packages genomicalignments (1.12.2) and genomicranges (1.28.4) from data downloaded through the gdc portal. expression data of the tumors from uvm_1 and gbm_4 was explored through the cbioportal. effect of splice mutations was predicted […]

PMCID: 5930521
PMID: 29716533
DOI: 10.1186/s12864-018-4699-5

[…] database [] and qtl were downloaded from the animal qtl database [] (based on the umd3.1 bovine reference genome assembly). the overlaps between cnv and genes or qtl were detected using r3.3.3 genomicranges []. to detect potential genes affected by significant cnv, we define the ‘overlap’ as more than 1 bp in common between the cnv region and the genomic region (including the 5-kb flanking […]

PMCID: 5928241
PMID: 29712937
DOI: 10.1038/s41598-018-24755-8

[…] downloaded as mapped bam files from the encode project website (https://www.encodeproject.org). the average tag densities surrounding each set of cpg sites were calculated in 20 bp bins using the genomicranges r package, and normalized to the total number of mapped reads., chromhmm chromatin state maps derived from normal human mammary epithelial cells (encff687qkv) were used to annotate […]

PMCID: 5928121
PMID: 29712907
DOI: 10.1038/s41467-018-04130-x

[…] we used the file peaks_gm12878.fasta and obtained the positions of the domains from the headers. the overlap between the two was computed with custom r scripts using the package genomicranges., to compute the rates of contact decay, the raw hi-c reads were normalized in 50 kb windows using the tadbit pipeline with default parameters. the contact decays were estimated using […]


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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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