IQuant: A fast yet accurate GUI tool for transcript quantification

Tin Chi Nguyen; Nan Deng; Guorong Xu; Zhansheng Duan; Dongxiao Zhu

doi:10.1109/BIBMW.2011.6112556

IQuant: A fast yet accurate GUI tool for transcript quantification

Tin Chi Nguyen
, Nan Deng
, Guorong Xu
, Zhansheng Duan
, Dongxiao Zhu

Wayne State University
University of New Orleans

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

1 Scopus citations

Abstract

Transcript quantification using RNA-seq is central to contemporary and future transcriptomics research. The existing tools are useful but have much room for improvement. We present a new statistical model, a fast yet accurate transcript quantification algorithm. Our tool takes RNA-seq reads in fasta or fastq format as input and output transcript abundance through a few mouse clicks. Our method compares favorably with the existing GUI tools in terms of both time complexity and accuracy. Availability: Both simulation data used for method comparisons and the GUI tool are freely available at http://asammate. sourceforge.net/.

Original language	English
Title of host publication	2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages	1048-1050
Number of pages	3
DOIs	https://doi.org/10.1109/BIBMW.2011.6112556
State	Published - 2011
Externally published	Yes
Event	2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States Duration: 12 Nov 2011 → 15 Nov 2011

Publication series

Name	2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011

Conference

Conference	2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011
Country/Territory	United States
City	Atlanta, GA
Period	12/11/11 → 15/11/11

Keywords

GUI
RNA-seq
Transcriptome quantification
alternative splicing
constrained least square

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10.1109/BIBMW.2011.6112556

Cite this

Nguyen, T. C., Deng, N., Xu, G., Duan, Z., & Zhu, D. (2011). IQuant: A fast yet accurate GUI tool for transcript quantification. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 (pp. 1048-1050). Article 6112556 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011). https://doi.org/10.1109/BIBMW.2011.6112556

@inproceedings{b3536f79c1cc4ccf9c79da0e2ee44d67,

title = "IQuant: A fast yet accurate GUI tool for transcript quantification",

abstract = "Transcript quantification using RNA-seq is central to contemporary and future transcriptomics research. The existing tools are useful but have much room for improvement. We present a new statistical model, a fast yet accurate transcript quantification algorithm. Our tool takes RNA-seq reads in fasta or fastq format as input and output transcript abundance through a few mouse clicks. Our method compares favorably with the existing GUI tools in terms of both time complexity and accuracy. Availability: Both simulation data used for method comparisons and the GUI tool are freely available at http://asammate. sourceforge.net/.",

keywords = "GUI, RNA-seq, Transcriptome quantification, alternative splicing, constrained least square",

author = "Nguyen, \{Tin Chi\} and Nan Deng and Guorong Xu and Zhansheng Duan and Dongxiao Zhu",

year = "2011",

doi = "10.1109/BIBMW.2011.6112556",

language = "英语",

isbn = "9781457716133",

series = "2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011",

pages = "1048--1050",

booktitle = "2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011",

note = "2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 ; Conference date: 12-11-2011 Through 15-11-2011",

}

Nguyen, TC, Deng, N, Xu, G, Duan, Z & Zhu, D 2011, IQuant: A fast yet accurate GUI tool for transcript quantification. in 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011., 6112556, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011, pp. 1048-1050, 2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011, Atlanta, GA, United States, 12/11/11. https://doi.org/10.1109/BIBMW.2011.6112556

IQuant: A fast yet accurate GUI tool for transcript quantification. / Nguyen, Tin Chi; Deng, Nan; Xu, Guorong et al.
2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 1048-1050 6112556 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - IQuant

T2 - 2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011

AU - Nguyen, Tin Chi

AU - Deng, Nan

AU - Xu, Guorong

AU - Duan, Zhansheng

AU - Zhu, Dongxiao

PY - 2011

Y1 - 2011

N2 - Transcript quantification using RNA-seq is central to contemporary and future transcriptomics research. The existing tools are useful but have much room for improvement. We present a new statistical model, a fast yet accurate transcript quantification algorithm. Our tool takes RNA-seq reads in fasta or fastq format as input and output transcript abundance through a few mouse clicks. Our method compares favorably with the existing GUI tools in terms of both time complexity and accuracy. Availability: Both simulation data used for method comparisons and the GUI tool are freely available at http://asammate. sourceforge.net/.

AB - Transcript quantification using RNA-seq is central to contemporary and future transcriptomics research. The existing tools are useful but have much room for improvement. We present a new statistical model, a fast yet accurate transcript quantification algorithm. Our tool takes RNA-seq reads in fasta or fastq format as input and output transcript abundance through a few mouse clicks. Our method compares favorably with the existing GUI tools in terms of both time complexity and accuracy. Availability: Both simulation data used for method comparisons and the GUI tool are freely available at http://asammate. sourceforge.net/.

KW - GUI

KW - RNA-seq

KW - Transcriptome quantification

KW - alternative splicing

KW - constrained least square

UR - https://www.scopus.com/pages/publications/84855993423

U2 - 10.1109/BIBMW.2011.6112556

DO - 10.1109/BIBMW.2011.6112556

M3 - 会议稿件

AN - SCOPUS:84855993423

SN - 9781457716133

T3 - 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011

SP - 1048

EP - 1050

BT - 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011

Y2 - 12 November 2011 through 15 November 2011

ER -

IQuant: A fast yet accurate GUI tool for transcript quantification

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Keywords

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