All the tools you need to analyse your miRNAs

iMir


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


Analysis Scheme:
iMir is a modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, differential expression analysis, biological target prediction and other useful options by integrating multiple open source modules and resources in an automated workflow.

Homepage: Link

Last Software Update: Jan. 2, 2015
Publication Date: Dec. 13, 2013
Citations: 20 [via Pubmed]

Organism Specific:
  • any

  • Reference Genome Needed: (if other specie than human, mouse and rat is analysed)
    Online/Local: /
    Installation/User Level: advanced
    User Adjustability:
    User support:
    Precomputed Target Results Available For Download:
    License: GPLv3
    Target Prediction
    Algorithm Features:
  • seed match
  • conservation
  • free energy
  • target-site abundance
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content

  • Target Region: 3'UTR, CDS
    Target Annotation:
    Algorithm: TargetScan, miRanda
    NGS Data Needed:
    Metaserver:
    Sequencing Analysis
    Algorithm Features:
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • precursor prediction
  • isomiRs identyfication
  • 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: DESeq, Fisher's Exact Test
    miRNA differential expression:
    mRNA differential expression:
    NGS Data Needed:
    Known miRNA Identification
    NGS Data Needed:
    IsomiRs Identification
    NGS Data Needed:





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