IDP-fusion statistics

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Citations per year

Number of citations per year for the bioinformatics software tool IDP-fusion
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Tool usage distribution map

This map represents all the scientific publications referring to IDP-fusion per scientific context
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IDP-fusion specifications

Information


Unique identifier OMICS_08780
Name IDP-fusion
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Requirements
Scipy, Numpy, seqmap, Bowtie, STAR, GMAP or BLAT
Maintained Yes

Versioning


No version available

Maintainer


Publication for IDP-fusion

IDP-fusion citations

 (5)
library_books

Gaining comprehensive biological insight into the transcriptome by performing a broad spectrum RNA seq analysis

2017
Nat Commun
PMCID: 5498581
PMID: 28680106
DOI: 10.1038/s41467-017-00050-4

[…] Several tools have been proposed to identify fusion from transcriptomic data such as JAFFA, STAR-Fusion, TopHat-Fusion, FusionCatcher, and SOAPfuse. In addition to these short-read-based techniques, IDP-fusion, and Iso-Seq methods can analyse long-read RNA-seq data to identify fused genes.Here we assessed these approaches in detecting the 71 validated gene fusions in the MCF-7 breast cancer cell- […]

library_books

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

2017
F1000Res
PMCID: 5553090
PMID: 28868132
DOI: 10.5256/f1000research.11392.r19894

[…] dies using PacBio or ONT alone, Hybrid-Seq can reduce the requirement of data size and improve the output, especially for transcriptome-wide studies. For example, a series of Hybrid-Seq methods (IDP, IDP-fusion, IDP-ASE) have been developed to improve the transcriptome studies to isoform levels (e.g., gene isoform reconstruction, fusion genes and allele phasing) with higher sensitivity and accurac […]

library_books

IDP ASE: haplotyping and quantifying allele specific expression at the gene and gene isoform level by hybrid sequencing

2016
Nucleic Acids Res
PMCID: 5952581
PMID: 27899656
DOI: 10.1093/nar/gkw1076

[…] TGS-only analysis and can improve the overall performance and resolution of the output data. In particular, a series of bioinformatics tools for Hybrid-Seq transcriptome data, including LSC, IDP and IDP-fusion, have been demonstrated to elucidate transcriptomes at the gene isoform level with high precision and sensitivity (,–).Here, we present a new method (termed IDP-ASE, http://www.healthcare.u […]

library_books

Discovering and understanding oncogenic gene fusions through data intensive computational approaches

2016
Nucleic Acids Res
PMCID: 4889949
PMID: 27105842
DOI: 10.1093/nar/gkw282

[…] r () and CREST (), can call gene fusions in addition to other structural rearrangements. In the last 2 years, several additional fusion mapping tools have been released—FusionMetaCaller (), JAFFA (), IDP-fusion (), TRUP (), FusionCatcher and PRADA (). A number of supporting tools, such as the Bioconductor package Chimera (), offer utilities for organizing, analyzing and validating gene fusion list […]

library_books

PacBio Sequencing and Its Applications

2015
PMCID: 4678779
PMID: 26542840
DOI: 10.1016/j.gpb.2015.08.002

[…] itate the development of models of differentiation and cell commitment within the developing embryo and a better understanding of the molecular mechanisms involved in the maintenance of pluripotency. IDP-fusion has also been recently released for the identification of fusion genes, fusion sites, and fusion gene isoforms from cancer transcriptomes . In the human MCF7 breast cancer cell line, IDP-fu […]


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IDP-fusion institution(s)
Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
IDP-fusion funding source(s)
The institutional fund of the Department of Internal Medicine, University of Iowa; National Institutes of Health [RO1GM109836, RO1HG007834]

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