This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Short Report
Marcelo F. Carazzolle
University of Campinas
Corresponding Author
ORCiD: https://orcid.org/0000-0002-5474-2830
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This work is licensed under a CC BY 4.0 License. Read Full License
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When comparing gene expression data of different tissues it is often interesting to identify tissue-specific genes or transcripts. Even though there are several metrics to measure tissue-specificity, a user-friendly tool that facilitates this analysis is not available yet. We present tspex, a software that allows easy computation of a comprehensive set of different tissue-specificity metrics from gene expression data. tspex can be used through a web interface, command-line or the Python API. Its package version also provides visualization functions that facilitate inspection of results. The documentation and the source code of tspex are available at https://apcamargo.github.io/tspex/ and the web application can be accessed at https://tspex.lge.ibi.unicamp.br/
Keywords
RNA-Seq, transcription, quantification, software, bioinformatics, program
Figure 1
This is a list of supplementary files associated with this preprint. Click to download.
- tspexformulas.pdf
Supplementary Material: Formulas of Tissue-specificity metrics implemented in tspex
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Short Report
Marcelo F. Carazzolle
University of Campinas
Corresponding Author
ORCiD: https://orcid.org/0000-0002-5474-2830
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 04 Aug, 2020
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Declarations:
Declarations
- The author has confirmed that a statement listing potential conflicts of interest or lack thereof is included in the text.
When comparing gene expression data of different tissues it is often interesting to identify tissue-specific genes or transcripts. Even though there are several metrics to measure tissue-specificity, a user-friendly tool that facilitates this analysis is not available yet. We present tspex, a software that allows easy computation of a comprehensive set of different tissue-specificity metrics from gene expression data. tspex can be used through a web interface, command-line or the Python API. Its package version also provides visualization functions that facilitate inspection of results. The documentation and the source code of tspex are available at https://apcamargo.github.io/tspex/ and the web application can be accessed at https://tspex.lge.ibi.unicamp.br/
Figure 1
This is a list of supplementary files associated with this preprint. Click to download.
- tspexformulas.pdf
Supplementary Material: Formulas of Tissue-specificity metrics implemented in tspex
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