CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data

SUMMARY: Next-generation sequencing has been widely applied to understand the complexity of non-coding RNAs (ncRNAs) in the last decades. Here, we present CPSS 2.0, an updated version of CPSS 1.0 for small RNA sequencing data analysis, with the following improvements: (i) a substantial increase of s...

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Detalles Bibliográficos
Autores principales: Wan, Changlin, Gao, Jianing, Zhang, Huan, Jiang, Xiaohua, Zang, Qiguang, Ban, Rongjun, Zhang, Yuanwei, Shi, Qinghua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860027/
https://www.ncbi.nlm.nih.gov/pubmed/28177064
http://dx.doi.org/10.1093/bioinformatics/btx066
Descripción
Sumario:SUMMARY: Next-generation sequencing has been widely applied to understand the complexity of non-coding RNAs (ncRNAs) in the last decades. Here, we present CPSS 2.0, an updated version of CPSS 1.0 for small RNA sequencing data analysis, with the following improvements: (i) a substantial increase of supported species from 10 to 48; (ii) improved strategies applied to detect ncRNAs; (iii) more ncRNAs can be detected and profiled, such as lncRNA and circRNA; (iv) identification of differentially expressed ncRNAs among multiple samples; (v) enhanced visualization interface containing graphs and charts in detailed analysis results. The new version of CPSS is an efficient bioinformatics tool for users in non-coding RNA research. AVAILABILITY AND IMPLEMENTATION: CPSS 2.0 is implemented in PHP + Perl + R and can be freely accessed at http://114.214.166.79/cpss2.0/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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