All the tools you need to analyse your miRNAs


Novel miRNA/Precursor Prediction Sequencing Analysis Differential Expression Analysis Known miRNA Identification

Analysis Scheme:
Comprehensive analysis pipeline for deep microRNA sequencing (CAP-miRSeq) integrates read preprocessing, alignment, mature/precursor/novel miRNA qualification, variant detection in miRNA coding region, and flexible differential expression between experimental conditions. According to computational infrastructures, users can run samples sequentially or in parallel for fast processing. In either a case, summary and expression reports for all samples are generated for easier quality assessment and downstream analyses.

Homepage: Link

Last Software Update: Sept. 3, 2014
Publication Date: June 3, 2014
Citations: 93 [via Pubmed]

Organism Specific:
  • any (from miRBase)

  • Reference Genome Needed:
    Online/Local: /
    Installation/User Level: advanced
    User Adjustability:
    User support:
    Precomputed Target Results Available For Download:
    License: GPL
    Sequencing Analysis
    Algorithm Features:
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • precursor prediction
  • other ncRNA identification

  • Sequencing Platform Specific: any
    PARE/CLIP-Seq: /
    Novel miRNA/Precursor Prediction
    Prediction Features:
  • structure
  • conservation

  • Algorithm: miRDeep2 method
    Novel miRNA / Precursor Analysis: Prediction
    NGS Data Needed:
    Differential Expression Analysis
    Algorithm: edgeR
    miRNA differential expression:
    mRNA differential expression:
    NGS Data Needed:
    Known miRNA Identification
    NGS Data Needed:

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