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GenomicInteractions specifications

Information


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


No version available

Documentation


Publication for GenomicInteractions

GenomicInteractions citations

 (4)
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

[…] pendencies 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
Mol Syst Biol
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 a […]

library_books

Infrastructure for genomic interactions: Bioconductor classes for Hi C, ChIA PET and related experiments

2016
F1000Res
PMCID: 4890298
PMID: 27303634
DOI: 10.5256/f1000research.9426.r13924

[…] nside the nucleus. The analysis of Hi-C and ChIA-PET data is not a trivial task, and many software packages have been developed to facilitate this process. Several of these packages like diffHic and GenomicInteractions are part of the open-source Bioconductor project, which aims to provide accessible tools for analyzing high-throughput genomic data with the R programming language. One of the str […]

library_books

Promoter like epigenetic signatures in exons displaying cell type specific splicing

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

[…] 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 []. […]

Citations

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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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