Repository revision
repository tip
Select a revision to inspect and download versions of Galaxy utilities from this repository.

Repository cpat
Name: cpat
Owner: bgruening
Synopsis: Coding-potential assessment tool using an alignment-free logistic regression model.
CPAT is a bioinformatics tool to predict RNAs coding
probability based on the RNA sequence characteristics.
To achieve this goal, CPAT calculates scores of these 4
linguistic features from a set of known protein-coding
genes and another set of non-coding genes: ORF size, ORF
coverage, Fickett TESTCODE and hexamer usage bias.
CPAT will then builds a logistic regression model using these 4
features as predictor variables and the protein-coding
status as the response variable. After evaluating the
performance and determining the probability cutoff,
the model can be used to predict new RNA sequences.
Content homepage: https://github.com/liguowang/cpat
Development repository: https://github.com/bgruening/galaxytools/tree/master/tools/cpat
Link to this repository: https://toolshed.g2.bx.psu.edu/view/bgruening/cpat/7ccc6234b54e
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/cpat
Type: unrestricted
Revision: 2:7ccc6234b54e
This revision can be installed: True
Times cloned / installed: 168

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
coding potential assessment 3.0.5+galaxy1 16.01

Categories
Transcriptomics - Tools for use in the study of Transcriptomics.