piPipes

piPipes is a set of coordinated pipelines designed to analyze and interpret piRNA and transposon-derived RNA sequencing data from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome, CAGE, ChIP, and genomic DNA-seq. It is aimed at standardizing computational methods in the piRNA field and provides figures and tables suitable for publication. piPipes is useful for extracting useful information from gigabytes of sequencing data, and it facilitates data analysis by researchers with varying levels of computational skills.

Topic

ChIP-seq;Functional, regulatory and non-coding RNA;Gene expression;RNA;DNA;Sequencing

Detail

  • Operation: Gene expression analysis

  • Software interface: Command-line user interface

  • Language: R;C;Python;Shell;C++;Perl

  • License: GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.5.0

  • Credit: National Institutes of Health.

  • Input: -

  • Output: -

  • Contact: piPipesQ@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.
  • Han BW, et al. piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. 2015; 31:593-5. doi: 10.1093/bioinformatics/btu647
  • https://doi.org/10.1093/bioinformatics/btu647
  • PMID: 25342065
  • PMC: PMC4325541

Download and documentation

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