https://github.com/compomics/pride-asa-pipeline

Uniform annotation of identified spectra.
https://github.com/compomics/pride-asa-pipeline

Last synced: about 2 months ago
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Uniform annotation of identified spectra.

• Host: GitHub
• URL: https://github.com/compomics/pride-asa-pipeline
• Owner: CompOmics
• Created: 2015-06-17T12:13:32.000Z (almost 11 years ago)
• Default Branch: master
• Last Pushed: 2021-10-12T10:22:31.000Z (over 4 years ago)
• Last Synced: 2025-09-10T05:09:44.193Z (7 months ago)
• Language: Java
• Homepage:
• Size: 162 MB
• Stars: 1
• Watchers: 17
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE-2.0.txt

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README

          
# pride-asa-pipeline

![logo](http://genesis.ugent.be/uvpublicdata/pride-asa-pipeline/pride-asa-pipeline-logo.png) 

 * [Project Description](#project-description)

 * [Downloads](#downloads)

 * [Usage](#usage)

 * [Troubleshooting](#troubleshooting)

 * [Related Projects](#related-projects)

 * [Project Support](#project-support)

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## Project Description

Pride-asap is a library written in Java that provides a uniform annotation of identified spectra stored in PRIDE. The application can be ran in a command line mode for automated processing of multiple PRIDE experiments, but also has a graphical user interface that allows end users to annotate the spectra in PRIDE experiments and to inspect the results in detail.

### Citation

 * [Hulstaert et al: J Proteomics. 2013 Apr 17. pii: S1874-3919(13)00192-9](http://www.ncbi.nlm.nih.gov/pubmed/23603108)

 * If you use pride-asa-pipeline as part of a paper, please include the reference above.

[Go to top of page](#pride-asa-pipeline)

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## Downloads

Download pride-asa-pipeline 1.5.11 [here](https://genesis.ugent.be/maven2/com/compomics/pride-asa-pipeline/1.5.11/pride-asa-pipeline-1.5.11.zip). 

[Go to top of page](#pride-asa-pipeline)

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## Usage

The pride-asa-pipeline jar file and all the libraries needed to run the tool. Double clicking this resulting jar file will start the pipeline. See the [manual](https://github.com/compomics/pride-asa-pipeline/wiki/Manual) for additional information on how to run and configure the pipeline.

[Go to top of page](#pride-asa-pipeline)

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## Troubleshooting

Please report any issues or requests in the [issues section](https://github.com/compomics/pride-asa-pipeline/issues). We will attempt to come up with a solution as soon as possible.

[Go to top of page](#pride-asa-pipeline)

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## Related Projects

The pride-asa-pipeline makes use of [compomics-utilities](http://code.google.com/p/compomics-utilities).

You might also find some of the following projects interesting: [Peptizer](http://code.google.com/p/peptizer), [dbtoolkit](https://github.com/compomics/dbtoolkit),

[ms-lims](http://code.google.com/p/ms-lims),

[Rover](http://code.google.com/p/compomics-rover) and

[PeptideShaker](http://code.google.com/p/peptide-shaker).

[Go to top of page](#pride-asa-pipeline)

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## Project Support

The pride-asa-pipeline project is grateful for the support by:

| Compomics | VIB | Ghent University|

|:--:|:--:|:--:|

| [![compomics](http://genesis.ugent.be/uvpublicdata/image/compomics.png)](http://www.compomics.com) | [![vib](http://genesis.ugent.be/uvpublicdata/image/vib.png)](http://www.vib.be) | [![ugent](http://genesis.ugent.be/uvpublicdata/image/ugent.png)](http://www.ugent.be/en) |

[Go to top of page](#pride-asa-pipeline)

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| IntelliJ | Netbeans | Java | Maven |

|:--:|:--:|:--:|:--:|

| [![intellij](https://www.jetbrains.com/idea/docs/logo_intellij_idea.png)](https://www.jetbrains.com/idea/) | [![netbeans](https://netbeans.org/images_www/visual-guidelines/NB-logo-single.jpg)](https://netbeans.org/) | [![java](http://genesis.ugent.be/uvpublicdata/image/java.png)](http://java.com/en/) | [![maven](http://genesis.ugent.be/uvpublicdata/image/maven.png)](http://maven.apache.org/) |

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