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GenomicInteractions specifications

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Unique identifier OMICS_10738
Name GenomicInteractions
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
Requirements
methods, stats, grid, graphics, Biobase, IRanges, Rsamtools, utils, testthat, GenomeInfoDb, rtracklayer, BiocStyle, grDevices, R(>=3.5), dplyr, ggplot2, Gviz, data.table, knitr, BiocGenerics(>=0.15.3), stringr, igraph, gridExtra, S4Vectors(>=0.13.13), InteractionSet, GenomicRanges(>=1.29.6)
Maintained Yes

Versioning


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Documentation


Publication for GenomicInteractions

GenomicInteractions citations

 (3)
library_books

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

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

[…] from bioconductor 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")) , […]

library_books

Pervasive coexpression of spatially proximal genes is buffered at the protein level

2017
PMCID: 5572396
PMID: 28835372
DOI: 10.15252/msb.20177548

[…] genome coordinates. grch37 transcription start sites for all genes were obtained using the biomart r package (durinck et al, ), considering only the tss of the outermost transcript of each gene. the genomicinteractions r package (harmston et al, ) was used to determine the contact frequency between the genes in our dataset, considering the median read count of all hi‐c pixels in a range ± 40 kb […]

library_books

Promoter like epigenetic signatures in exons displaying cell type specific splicing

2015
PMCID: 4619081
PMID: 26498677
DOI: 10.1186/s13059-015-0797-8

[…] used tss, besides the average signal from chia-pet experiments we also quantified the number of interactions found, per exon, with the un-phosphorylated ser2 polymerase ii using the r package genomicinteractions []., alternative spliced exons differentially expressed between cell lines were partitioned according to their histone modifications and control levels using a k-means clustering […]


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GenomicInteractions institution(s)
Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, UK

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