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Curse : building expression atlases and co-expression networks from public RNA-Seq data

Dries Vaneechoutte (UGent) and Klaas Vandepoele (UGent)
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Abstract
Public RNA-Sequencing (RNA-Seq) datasets are a valuable resource for transcriptome analyses, but their accessibility is hindered by the imperfect quality and presentation of their metadata and by the complexity of processing raw sequencing data. The Curse suite was created to alleviate these problems. It consists of an online curation tool named Curse to efficiently build compendia of experiments hosted on the Sequence Read Archive, and a lightweight pipeline named Prose to download and process the RNA-Seq data into expression atlases and co-expression networks. Curse networks showed improved linking of functionally related genes compared to the state-of-the-art.; Availability and implementation: Curse, Prose, and their manuals are available at http://bioinformatics.psb.ugent.be/webtools/Curse/. Prose was implemented in Java.; Supplementary information: Supplementary data are available at Bioinformatics online.

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Citation

Please use this url to cite or link to this publication:

Chicago
Vaneechoutte, Dries, and Klaas Vandepoele. 2019. “Curse : Building Expression Atlases and Co-expression Networks from Public RNA-Seq Data.” Bioinformatics.
APA
Vaneechoutte, D., & Vandepoele, K. (2019). Curse : building expression atlases and co-expression networks from public RNA-Seq data. BIOINFORMATICS.
Vancouver
1.
Vaneechoutte D, Vandepoele K. Curse : building expression atlases and co-expression networks from public RNA-Seq data. BIOINFORMATICS. 2019;
MLA
Vaneechoutte, Dries, and Klaas Vandepoele. “Curse : Building Expression Atlases and Co-expression Networks from Public RNA-Seq Data.” BIOINFORMATICS (2019): n. pag. Print.
@article{8587983,
  abstract     = {Public RNA-Sequencing (RNA-Seq) datasets are a valuable resource for transcriptome analyses, but their accessibility is hindered by the imperfect quality and presentation of their metadata and by the complexity of processing raw sequencing data. The Curse suite was created to alleviate these problems. It consists of an online curation tool named Curse to efficiently build compendia of experiments hosted on the Sequence Read Archive, and a lightweight pipeline named Prose to download and process the RNA-Seq data into expression atlases and co-expression networks. Curse networks showed improved linking of functionally related genes compared to the state-of-the-art.; Availability and implementation: Curse, Prose, and their manuals are available at http://bioinformatics.psb.ugent.be/webtools/Curse/. Prose was implemented in Java.; Supplementary information: Supplementary data are available at Bioinformatics online.},
  author       = {Vaneechoutte, Dries and Vandepoele, Klaas},
  issn         = {1367-4811},
  journal      = {BIOINFORMATICS},
  language     = {eng},
  title        = {Curse : building expression atlases and co-expression networks from public RNA-Seq data},
  url          = {http://dx.doi.org/10.1093/bioinformatics/bty1052},
  year         = {2019},
}

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