iRegulon pipeline

iRegulon specifications

Information


Unique identifier OMICS_05264
Name iRegulon
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Requirements Cytoscape
Maintained Yes

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Documentation


Publication for iRegulon

iRegulon citations

 (2)
2017
PMCID: 5263231

[…] transcriptomes were analyzed by aligning reads to drosophila genome dm6 in tophat2, enumerating reads with htseq, and model fitting using deseq2. tf-binding motif enrichment was analyzed using iregulon. survival was analyzed in r and jmp. see supplemental experimental procedures for full details of animal husbandry, molecular, and data analysis., n.a. devised the study; a.j.d., m.e., […]

2015
PMCID: 4448502

[…] 67 binding domain motifs, with 47 unique transcription factors, were found. of these, srebp1 and srebp2 were pulled out at the top of the list. this was completed using a plugin for cytoscape called iregulon25 and the output is included in the supplemental as table st4. we combined genes regulated by srebp1/srebp2 and egr1/egr2 as well as fold change expression values for all three treatment […]

iRegulon institution(s)
Laboratory of Computational Biology, KU Leuven Center for Human Genetics, Leuven, Belgium; Laboratory for Molecular Cancer Biology, KU Leuven Center for Human Genetics, Leuven, Belgium

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