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Resource Type

  1. Algorithmic software component


  1. Resource Description
    "HAMR (High-throughput Annotation of Modified Ribonucleotides) is a web application that allows you to detect and classify modified nucleotides in RNA-seq data." "HAMR scans RNA-sequencing data for sites showing potential signatures of nucleotide modification. Simply point it to your RNA-seq data it will scan the entire transcriptome. You can also limit the analysis to particular genomic regions of interest, either by entering one or providing a BED file containing the intervals. The output is a table containing the list of sites with nucleotide patterns that deviate from expectation at a statistically significant rate."
  2. Additional Name
    High-throughput Annotation of Modified Ribonucleotides
  3. Used by
    Wang Laboratory
  4. Data Input
    RNA-seq data as a web accessible BAM file
  5. Data Input
    OPTIONAL: BED file containing a list of intervals to analyze
  6. Data Output
    List of sites with nucleotide patterns that deviate from expectation at a statistically significant rate
  7. Software purpose
    Sequence feature identification objective
  8. Related Publication or Documentation
    HAMR: high-throughput annotation of modified ribonucleotides
  9. Related Publication or Documentation
    Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis
  10. Website(s)
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Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016