RATs pipeline

RATs specifications

Information


Unique identifier OMICS_18188
Name RATs
Alternative name Relative Abundance of Transcripts
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Transcript abundance estimates with or without bootstrapping.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Version 0.4.4
Stability Stable
Requirements Data.table, MatrixStats, ggplot2, Shiny
Maintained Yes

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Documentation


Maintainer


  • person_outline Gordon Simpson <>

Publication for Relative Abundance of Transcripts

library_books

Identifying differential isoform abundance with RATs: a universal tool and a warning.

2017 BioRxiv
DOI: 10.1101/132761

RATs citation

2014
PMCID: 4321550

[…] (clc bio). the validity of the assembly was performed by remapping (clc genomic workbench) the original read onto the assembly and through functional annotation, with the former also providing a relative abundance of transcripts in the original sample. functional annotation was performed using blastx and was used to interrogate the non-redundant protein sequence data downloaded from ncbi (1 […]

RATs institution(s)
Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK; Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, UK; Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, UK; Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, UK
RATs funding source(s)
Supported by Wellcome Trust Strategic Awards [098439/Z/12/Z and WT097945], and Biotechnology and Biological Sciences Research Council Grants [BB/H002286/1; BB/J00247X/1; BB/M010066/1; BB/M004155/1].

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