CIPHER

CIPHER is a pipeline tool to analyze next-generation sequencing data and predict genomic regulatory elements interactively. CIPHER can use RNA-seq, ChIP-seq, DNase-seq, MNase-seq, GRO-seq, and ATAC-seq data as input. A typical workflow is as follows:
evaluation of raw sequences > trimming and adapter removal > mapping and filtering by quality > visualization track generation > quality control assessment.
The CIPHER algorithm includes various other essential functions.

Topic

ChIP-seq;RNA-seq;Gene regulation

Detail

  • Operation: Gene regulatory network analysis

  • Software interface: Command-line user interface

  • Language: R

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: The National Institute of Allergy and Infectious Diseases (NIAID) of the NIH.

  • Input: -

  • Output: -

  • Contact: cag104@ucsd.edu, Iván D’Orso Ivan.Dorso@utsouthwestern.edu

  • Collection: -

  • Maturity: -

Publications

  • CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction.
  • Guzman C, D'Orso I. CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction. BMC Bioinformatics. 2017 Aug 8;18(1):363. doi: 10.1186/s12859-017-1770-1. PMID: 28789639; PMCID: PMC5549294.
  • https://doi.org/10.1186/s12859-017-1770-1
  • PMID: 28789639
  • PMC: PMC5549294

Download and documentation

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