All the tools you need to analyse your miRNAs


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

Analysis Scheme:
An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data.

Homepage: Link

Last Software Update: May 22, 2013
Publication Date: May 17, 2012
Citations: 7 [via Pubmed]

Organism Specific:
  • plants
  • animals

  • Reference Genome Needed:
    Online/Local: /
    Installation/User Level: advanced
    User Adjustability:
    User support:
    Precomputed Target Results Available For Download:
    License: Apache License V2.0
    Input Data Required:
  • output file (e.g. in GFF format) from methods that map deep sequencing reads to reference genome

  • Sequencing Analysis
    Algorithm Features:
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • precursor prediction
  • isomiRs identyfication

  • Sequencing Platform Specific: Illumina, SOLiD
    PARE/CLIP-Seq: /
    Novel miRNA/Precursor Prediction
    Prediction Features:
  • sequence
  • structure

  • Algorithm: RNAfold
    Novel miRNA / Precursor Analysis: Prediction
    NGS Data Needed:
    Differential Expression Analysis
    Algorithm: DESeq, edgeR
    miRNA differential expression:
    mRNA differential expression:
    NGS Data Needed:
    Known miRNA Identification
    NGS Data Needed:
    IsomiRs Identification
    NGS Data Needed:

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