isomiRs Identification

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1 CPSS CPSS is (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission. /
  • human
  • mouse
  • rat
  • chicken
  • fish
  • other animals (selectable)

  • Homepage

    Publication
    May 9, 2012
    Citations: 18
    2 DeAnnIso DeAnnIso, is an online tool, that is designed for Detection and Annotation of IsomiR from small RNA sequencing data. The detected isomiRs will be classified into different categories. The isomiRs will be aligned with canonical miRNA, and will be annotated with expression, constitution, SNP, and an in-house dataset. It can also extract differentially expressing isomiR between two samples. In addition, IsomiR Bank provides targets prediction and enrichment analysis to evaluate the effects of isomiRs on target selection. /
  • human
  • mouse
  • fish
  • fly
  • plants (selectable)

  • Homepage

    Publication
    May 13, 2016
    Citations: 7
    3 iMir 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. /
  • any

  • (if other specie than human, mouse and rat is analysed)
    Homepage

    Publication
    Dec. 13, 2013
    Citations: 20
    4 isomiR2Function somiR2Function allows for the high-throughput detection of plant isomiRs from any miRNA-seq profiling study. isomiR2Function not only allows for the identification of the templated and non-templated 5′- isomiRs and 3′- isomiRs but also allows for the expression quantification. Since, the prediction of biologically relevant target is an important criterion for the identification of isomiRs and their targets - isomiR2Function identifies target as well. Following target prediction, it allows for functional enrichment of the identified targets. In parallel, isomiR2Function provides support for the visualization of read mapping on corresponding precursor sequences. /
  • plants

  • Homepage

    Publication
    March 21, 2017
    Citations: 0
    5 IsomiRage A workflow for the characterization and analysis of miRNAs and their variants in next-generation sequencing datasets. IsomiRage permits the deconvolution of miRNA heterogeneity and could be used to explore the functional role of miRNA isoforms. /
  • any

  • Homepage

    Publication
    Sept. 29, 2014
    Citations: 20
    6 isomiReX IsomiRex is a open-access web platform to identify isomiRs and on the fly graphical visualization of the differentially expressed miRNAs in control as well as treated library. /
  • any

  • Homepage

    Publication
    July 4, 2013
    Citations: 14
    7 miRge miRge is a logical, ultrafast, small RNA-seq solution to process samples in a highly multiplexed fashion, resulting in dramatically decreased computational requirements when processing sets of samples in a single run. It utilizes a unique sequential alignment algorithm for annotation of small RNA-seq data. Output is given for miRNAs as raw reads and reads per million (RPM) in addition to isomiR data and reads for all other RNA species (tRNA, rRNA, snoRNA, mRNA). IsomiR entropy can be determined for each sample or across samples in a multiplex run. /
  • any

  • Homepage

    Publication
    Nov. 16, 2015
    Citations: 22
    8 miRanalyzer miRanalyzer – a web server and stand-alone tool for the detection of known and prediction of new microRNAs in high-throughput sequencing experiments. /
  • human
  • mouse
  • rat
  • fly
  • worm
  • chicken
  • fish
  • other animals (selectable)
  • plants (selectable)

  • (online)

    (local)
    Homepage

    Publication
    April 22, 2011
    Citations: 113
    9 MIRPIPE MIRPIPE represents a new pipeline for the quantification of microRNA based on smallRNA sequencing reads. In opposition to present algorithms that generally rely on genomic data to identify miRNAs, MIRPIPE focuses on niche model organisms that lack such information. Among the MIRPIPE features are automatic trimming and adapter removal of raw RNA-Seq reads originating from various sequencing instruments, clustering of isomiRs, and quantification of detected miRNAs by homology search versus public or user uploaded reference databases. /
  • human
  • mouse
  • fly
  • fish
  • chicken
  • rat
  • any

  • Homepage

    Publication
    Aug. 26, 2016
    Citations: 8
    10 mirPRo mirPRo is a tool for miRNA-seq analysis. It can quantify known and novel miRNAs in single-end RNA-seq data and provide useful functions such as IsomiR detection and "arm switching" identification, miRNA family quantification, and read cataloging in terms of genome annotation. mirPRo only works for species that has reference genome. /
  • any

  • Homepage

    Publication
    Oct. 5, 2015
    Citations: 4
    11 miRSeqNovel An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. /
  • plants
  • animals

  • Homepage

    Publication
    May 17, 2012
    Citations: 4
    12 mirTools 2.0 MirTools 2.0 is updated version of mirTools, which was developed to comprehensive characterize the small RNA transcriptome obtained from high-throughput sequencing. It enables user to: detect and profile non-coding RNA (tRNA, snRNA, snoRNA, rRNA ans piRNA); obtain detailed annotation ifmromation about known miRNA (absolute/realtive reds count and most abundant tags); identify the microRNA targeted genes and their detailed functional annotate; perform the comparison of many samples and identify the differentially expressed non-coding RNAs between experimental groups; discovery the novel miRNAs. /
  • human
  • mouse
  • rat
  • chicken
  • fish
  • worm
  • fly
  • other animals (selectable)
  • plants (selectable)
  • any (local)

  • (online)

    (local)
    Homepage

    Publication
    May 29, 2013
    Citations: 28
    13 QuagmiR QuagmiR - the first cloud-based tool to analyze isomiRs from next generation sequencing data. Using a novel and flexible searching algorithm designated for the detection and annotation of isomiRs of heterogeneous nature. It permits extensive customization of the query process and reference databases to meet the user’s diverse demands. QuagmiR is written in Python and can be obtained freely from Github. QuagmiR can be run from command-line on local machines, as well as high performance servers. A web-accessible version of the tool has also been made available for use by academic researchers through the National Cancer Institute-funded Seven Bridges Cancer Genomics Cloud. /
  • Invertebrates
  • plants
  • Vertebrates
  • viruses
  • animals
  • mouse
  • fish
  • worm
  • rat
  • fly
  • human
  • chicken
  • any

  • Homepage

    Publication
    14 SeqBuster A command-line bioinformatic tool usefull for the analysis of deep sequencing data, namely known miRNAs and isomiRs annotation. /
  • any

  • Homepage

    Publication
    Dec. 11, 2009
    Citations: 60
    15 sRNAtoolbox sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and several downstream analysis tools. The center piece of sRNAtoolbox is sRNAbench, which allows the expression profiling and prediction of novel microRNAs in deep sequencing experiments. The other tools can be either launched on sRNAbench results, or independently using the appropriate file formats. /
  • human
  • mouse
  • rat
  • chicken
  • fly
  • fish
  • viruses
  • plants (selectable)
  • bacteria
  • other animals (selectable)

  • Homepage

    Publication
    May 27, 2015
    Citations: 46