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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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Documentation


Maintainer


  • person_outline Michael Lawrence

Publication for GenomicRanges

GenomicRanges citations

 (125)
library_books

Outlier response to anti PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors

2018
Nat Commun
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] d by 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 on […]

call_split

Plasma cell differentiation is controlled by multiple cell division coupled epigenetic programs

2018
Nat Commun
PMCID: 5923265
PMID: 29703886
DOI: 10.1038/s41467-018-04125-8
call_split See protocol

[…] ads 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 betwe […]

library_books

Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm

2018
GigaScience
PMCID: 5928411
PMID: 29635292
DOI: 10.1093/gigascience/giy039

[…] window by 50-bp steps until it contained less than 80% hypomethylated (methylation level <20%) CpGs. Only the HMRs with at least 5 CG detected with more than 5 × coverage were used for analysis. The GenomicRanges package in R was used to calculate statistics of the overlapped HMRs in different tissues or sperm. […]

library_books

Racial differences in endometrial cancer molecular portraits in The Cancer Genome Atlas

2018
Oncotarget
PMCID: 5908308
PMID: 29682207
DOI: 10.18632/oncotarget.24907

[…] using ten iterations. Genomic SCNA plots were generated using a custom R script, with cut-off defined also at FDR Q<0.15. Transcripts overlapping recurrent SCNA were defined using the biomaRt [] and GenomicRanges [] packages in R, with “ENSEMBL_MART_ENSEMBL”, “grch37.ensembl.org”, “/biomart/martservice”, and “hsapiens_gene_ensembl” set as the biomart, host, path, and dataset, respectively. […]

library_books

ATACseqQC: a Bioconductor package for post alignment quality assessment of ATAC seq data

2018
BMC Genomics
PMCID: 5831847
PMID: 29490630
DOI: 10.1186/s12864-018-4559-3

[…] he footprint analysis also leverages the matchPWM function in the BSgenome package [, ] to search potential binding sites for a given DNA-binding protein, represent the matched genomic coordinates as GenomicRanges objects, and plot the motif as a sequence logo using the motifStack package []. The factorFootprints function first uses the matchPWM function to predict the binding sites with an input […]

library_books

Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies

2018
F1000Res
PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] uctor and CRAN: source("https://bioconductor.org/biocLite.R") # uncomment the following line to install packages #biocLite(c("clusterProfiler", "DESeq2", "GenomicFeatures", "GenomicInteractions", "GenomicRanges", "ggplot2", "Gviz", "gwascat", "InteractionSet", "recount", "pheatmap", "RColorBrewer", "rtracklayer", "R.utils", "splitstackshape", "VariantAnnotation")) […]

Citations

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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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