Intervene specifications

Information


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

Download


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Versioning


No version available

Maintainer


  • person_outline Aziz Khan

Publication for Intervene

Intervene citations

 (2)
library_books

DNA methylation at enhancers identifies distinct breast cancer lineages

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

[…] all 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 pair) […]

library_books

The Schistosoma mansoni genome encodes thousands of long non coding RNAs predicted to be functional at different parasite life cycle stages

2017
Sci Rep
PMCID: 5585378
PMID: 28874839
DOI: 10.1038/s41598-017-10853-6

[…] on 3.3.2) with limma, edgeR, gplots and ggplot2 libraries loaded. Gene expression line charts were generated using matplotlib in Python. The intersection diagram in the UpSet format was plotted using Intervene (https://asntech.shinyapps.io/intervene/) (doi:10.1101/109728). […]

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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