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Bioinformatics. 2020 Mar 14. pii: btaa173. doi: 10.1093/bioinformatics/btaa173. [Epub ahead of print]

primirTSS: An R package for identifying cell-specific microRNA transcription start sites.

Author information

1
Nanjing University, School of Life Science.
2
High-Tech Research Institute of Nanjing University, Changzhou.

Abstract

SUMMARY:

The R/Bioconductor package primirTSS is a fast and convenient tool that allows implementation of the analytical method to identify transcription start sites of microRNAs by integrating ChIP-seq data of H3K4me3 and Pol II. It further ensures the precision by employing the conservation score and sequence features. The tool showed a good performance when using H3K4me3 or Pol II Chip-seq data alone as input, which brings convenience to applications where multiple data sets are hard to acquire. This flexible package is provided with both R-programming interfaces as well as graphical web interfaces.

AVAILABILITY:

primirTSS is available at: http://bioconductor.org/packages/primirTSS The documentation of the package including an accompanying tutorial was deposited at: https://bioconductor.org/packages/release/bioc/vignettes/primirTSS/inst/doc/primirTSS.html.

SUPPLEMENTARY INFORMATION:

Supplementary Data are available at Bioinformatics online.

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