primirTSS

primirTSS is an R package designed to identify transcription start sites (TSS) of microRNAs. The tool integrates ChIP-seq H3K4me3 and Pol II data, enhancing precision by incorporating conservation scores and sequence features. primirTSS demonstrates robust performance even with individual inputs of H3K4me3 or Pol II ChIP-seq data, providing flexibility for applications where acquiring multiple datasets may be challenging.

Topic

Functional, regulatory and non-coding RNA;Gene expression;ChIP-seq;RNA-Seq;Gene transcripts

Detail

  • Operation: miRNA expression analysis;miRNA target prediction;Deposition

  • Software interface: Command-line user interface

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.20.0

  • Credit: The National Science Foundation of China, the NJU-Yangzhou Institute of Optoelectronics, the National Science and Technology Major Project of China.

  • Input: -

  • Output: -

  • Contact: Pumin Li ipumin@163.com

  • Collection: -

  • Maturity: Stable

Publications

  • primirTSS: an R package for identifying cell-specific microRNA transcription start sites.
  • Li P, et al. primirTSS: an R package for identifying cell-specific microRNA transcription start sites. primirTSS: an R package for identifying cell-specific microRNA transcription start sites. 2020; 36:3605-3606. doi: 10.1093/bioinformatics/btaa173
  • https://doi.org/10.1093/BIOINFORMATICS/BTAA173
  • PMID: 32170928
  • PMC: -

Download and documentation

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