Haystack specifications


Unique identifier OMICS_22202
Name Haystack
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The genome-wide distributions of an epigenetic mark across multiple cell types or subjects as well as gene expression profiles quantified by microarray or RNA-seq.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 0.5.4
Stability Stable
aws, python, bedtools, scipy, numpy, conda, matplotlib, bioconda, pandas, sambamba, miniconda, anaconda, bx-python, webgraph, meme 4.11.2
Maintained Yes




No version available


  • person_outline Guo-Cheng Yuan
  • person_outline Luca Pinello

Publication for Haystack

Haystack institution(s)
Department of Molecular Pathology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical, School, Boston, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Harvard School of Public Health, Boston, MA, USA
Haystack funding source(s)
Supported by National Institutes of Health award R00HG008399 and R01HG009663.

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