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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
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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Maintainer
- person_outline Patrick BF O'Connor
Additional information
Publication for Ribo-Seq Unit Step Transformation
Comparative survey of the relative impact of mRNA features on local ribosome profiling read density
RUST citations
(2)Genome wide identification and differential analysis of translational initiation
[…] 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 […]
Translational contributions to tissue specificity in rhythmic and constitutive gene expression
[…] ame and nucleotide periodicity analyses were performed as in []. PCA relied on a combined matrix of CDS counts for RPF and RNA from both liver and kidney and following the same approach as before []. Ribo-seq Unit Step Transformation (RUST) analysis was used to assess whether the sequencing libraries were globally of similar quality in terms of their local footprint densities []. RUST is a simple […]
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