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SEECER

Performs error correction in RNA-Seq data. SEECER is a method based on profile a hidden Markov Model (HMMs). This method does not require a reference genome. It can handle non-uniform coverage and alternative splicing, both key challenges when performing RNA-Seq. This application is applicable to de novo RNA-Seq because it does not rely on a reference genome.

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SEECER forum

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SEECER classification

SEECER specifications

Unique identifier:
OMICS_26081
Software type:
Application/Script
Restrictions to use:
None
Programming languages:
R
Version:
0.1.3
Requirements:
GNU Scientific Library, SeqAn, JELLYFISH, OPENMP API
Name:
SEquencing Error CorrEction for Rna reads
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

SEECER distribution

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SEECER support

Documentation

Maintainer

  • Ziv Bar-Joseph <>

Credits

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Publications

Institution(s)

Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA; Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA

Funding source(s)

Supported by National Institutes of Health (NIH) [1RO1 GM085022] and National Science Foundation (NSF) [DBI-0965316 award].

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