riboHMM statistics

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Citations per year

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Tool usage distribution map

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Associated diseases

Associated diseases

riboHMM specifications


Unique identifier OMICS_20318
Name riboHMM
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Jothan K. Pritchard <>
  • person_outline Anil Raj <>
  • person_outline Sidney Wang <>
  • person_outline Yoav Gilad <>

Publication for riboHMM

riboHMM in publications

PMCID: 5701008
PMID: 29170441
DOI: 10.1038/s41467-017-01981-8

[…] frame (fig. ). to evaluate the performance of ribo-tish in predicting orfs from rribo-seq data, we performed an roc analysis for ribo-tish and four other published methods: ribotaper; orf-rater; ribohmm; and riborf using a published rribo-seq data set (methods). like ribo-tish, ribotaper, orf-rater, and ribohmm can predict orfs from rribo-seq data without user-specified orf candidates. […]

PMCID: 5314775
PMID: 27923997
DOI: 10.1093/nar/gkw1190

[…] stand alone tools were developed for differential gene expression analysis (anota (), babel (), ribodiff (), xtail ()), and for the prediction of translated orfs (ribotaper (), orf-rator () and ribohmm ()). ribomap () estimates footprint origins in the presence of multiple splice isoforms and repetitive regions and rfoot () uses riboseq data to predict non-ribosome protected rna sites. […]

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riboHMM institution(s)
Department of Genetics, Stanford University, Stanford, CA, USA; Department of Human Genetics, University of Chicago, Chicago, MA, USA; Department of Biology, Stanford University, Stanford, CA, USA; Department of Statistics, University of Chicago, Chicago, MA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
riboHMM funding source(s)
Supported by the National Institutes of Health (grant reference number HG007036), the National Institutes of Health (grant reference number MH084703), the National Institutes of Health (grant reference number HG02585).

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