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HAMR

eagle-i ID

http://eagle-i.itmat.upenn.edu/i/00000142-ba1e-0965-91c7-0c6080000000

Resource Type

  1. Algorithmic software component

Properties

  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)
    http://tesla.pcbi.upenn.edu/hamr/
 
RDFRDF
 
Provenance Metadata About This Resource Record
  1. workflow state
    Published
  2. contributor
    fcoldren
  3. created
    2013-12-03T15:22:29.195-05:00
  4. creator
    fcoldren
  5. modified
    2015-11-24T15:11:05.542-05:00

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The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016