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IsoLasso | A LASSO regression approach to RNA-Seq based transcriptome assembly

An algorithm used to assemble transcripts and estimate their expression levels from RNA-Seq reads. Three mains goals are reached by IsoLasso: the maximization of prediction accuracy, minimization of interpretation, and maximization of completeness. Experiments on simulated and real RNA-Seq datasets show that this software is able to make sets of assembled transcripts as complete as possible.

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IsoLasso classification

IsoLasso specifications

Unique identifier:
OMICS_01320
Interface:
Command line interface
Input format:
SAM
Programming languages:
C++
Version:
2.6.1
Requirements:
SAMtools, Libgsl-dev, Libcgal-dev
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
Source code URL:
http://alumni.cs.ucr.edu/~liw/isolasso-2.6.1.tar.gz

IsoLasso distribution

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Credits

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Publications

Institution(s)

Department of Computer Science and Engineering, University of California, Riverside, CA, USA; School of Life Science and Technology, Tongji University, Shanghai, China; School of Information Science and Technology, Tsinghua University, Beijing, China

Funding source(s)

Funded by the NSF (grant IIS-0711129) and the NIH (grant AI078885).

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