RUST specifications

Information


Unique identifier OMICS_12938
Name RUST
Alternative name Ribo-Seq Unit Step Transformation
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Patrick BF O'Connor

Additional information


Web application: http://ribogalaxy.ucc.ie/

Information


Unique identifier OMICS_12938
Name RUST
Alternative name Ribo-Seq Unit Step Transformation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2
Stability Stable
Requirements
BioPython, matplotlib, mock, pysam
Source code URL https://files.pythonhosted.org/packages/c3/ff/1ffe5c38505fd5226e344aaf91fd43dc38648ccf79ae7096ea0fa4f7f815/RUST-0.1.1.tar.gz
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Patrick BF O'Connor

Additional information


Web application: http://ribogalaxy.ucc.ie/

Publication for Ribo-Seq Unit Step Transformation

RUST citations

 (2)
library_books

Genome wide identification and differential analysis of translational initiation

2017
Nat Commun
PMCID: 5701008
PMID: 29170441
DOI: 10.1038/s41467-017-01981-8

[…] bserved signals in ribo-seq data. To reveal the sequence determinants of the RPF read density and help identify potential technical biases or artifacts in ribo-seq data, O’Connor et al. developed the ribo-seq unit step transformation (RUST) method, a normalization method that was based on the Heaviside step function and that performed better than other methods in the presence of heterogeneous nois […]

library_books

Translational contributions to tissue specificity in rhythmic and constitutive gene expression

2017
Genome Biol
PMCID: 5473967
PMID: 28622766
DOI: 10.1186/s13059-017-1222-2

[…] the kidney time series for both RNA-seq and RPF-seq data indicated excellent biological and technical reproducibility (Additional file : Figure S3A, B). We also used a recently developed tool, termed Ribo-seq Unit Step Transformation (RUST) [], to confirm high technical similarity of datasets between organs (Additional file : Figure S2C, D). Finally, principal component analysis (PCA) on all avail […]

RUST institution(s)
School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; Belozersky Institute, Lomonosov Moscow State University, Moscow, Russia
RUST funding source(s)
This work was supported by grants from Science Foundation Ireland (12/IA/1335) and the Wellcome Trust (094423).

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