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Intervene specifications

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Unique identifier OMICS_16307
Name Intervene
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Requires genomic regions or lists of genes/names as input.
Input format BED, GFF, GTF
Output data Outputs publication quality figures, intersection matrices, and R scripts to further enable and facilitate plot customization.
Output format R
Operating system Unix/Linux
Programming languages Python, R
Computer skills Advanced
Stability Stable
Requirements
Bedtools, pybedtools, Pandas, R::UpSetR, corrplot
Maintained Yes

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Publication for Intervene

Intervene citations

 (2)
library_books

Long Noncoding RNAs in Yeast Cells and Differentiated Subpopulations of Yeast Colonies and Biofilms

2018
PMCID: 5889882
PMID: 29765496
DOI: 10.1155/2018/4950591

[…] were annotated with functional categories using information in sgd (http://www.yeastgenome.org/, []) and the literature. datasets of differentially expressed (de) genes were then compared using intervene's upset module [], which visualizes the intersection of multiple data sets in upset plots (). no common antiregulated and only 6 common coregulated lncrna/gene pairs were identified in u15 […]

library_books

DNA methylation at enhancers identifies distinct breast cancer lineages

2017
PMCID: 5680222
PMID: 29123100
DOI: 10.1038/s41467-017-00510-x

[…] illumina infinium humanmethylation450 beadchip cpgs as background (supplementary data ). supplementary fig.  was constructed using data sets showing a hypergeometric log10 p-value < −100 with the intervene tool to obtain a svg figure further edited for colors using inkscape (https://inkscape.org/en/). we retrieved chia-pet pol2 loops in the mcf7 cell lines from encode, an emqtl (cpg-gene […]


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Intervene institution(s)
Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
Intervene funding source(s)
This work has been supported by the Norwegian Research Council, Helse Sør-Øst, and the University of Oslo through the Centre for Molecular Medicine Norway (NCMM), which is part of the Nordic European Molecular Biology Laboratory partnership for Molecular Medicine.

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