CPSS can analyze the small RNA deep sequencing data in different architecture: Single and Paired.
"Single" means the dataset of one sample, and "Paired" means the datasets of two samples.
By using CPSS, small RNA NGS data can be analyzed systematically in one platform after a single submission of data by integration of annotation and functional analysis of novel and/or differentially expressed miRNAs. CPSS generates an analysis report including: 1) annotation analysis, which provides a comprehensive analysis for small RNA transcriptome, such as the length distribution and genome mapping of the sequencing reads, small RNA annotation, prediction of novel miRNAs, identification of differentially expressed miRNAs, piRNAs and other small RNAs between samples, and detection of miRNA SNPs and isoforms; 2) functional analysis, which provides the functional analysis of miRNAs, e.g. predicting miRNA target genes by multi-tools, enriching Gene Ontology terms (GO), performing signalling pathways, and protein-protein interaction (PPI) analysis for the predicted genes.
Citation：Bioinformatics. 2012 Jul 15;28(14):1925-7. doi: 10.1093/bioinformatics/bts282. Epub 2012 May 9.