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SPLICE-q is a fast and user-friendly Python tool for genome-wide SPLICing Efficiency quantification

Project description


A Python tool for genome-wide SPLIcing Efficiency quantification from RNA-seq data.

User Manual


  • Quantification of individual intron splicing efficiencies from strand-specific RNA-seq data.
  • Sensitive to the overlap of genomic elements.
  • Fast and user-friendly.


SPLICE-q can be installed from pip and from source.


Using pip is the easiest way to install SPLICE-q.

 $ pip3 install SPLICE-q

Development/install from source

 $ git clone
 $ cd SPLICE-q
 $ pip3 install -e .


  • Python 3.6+
  • PySam
  • InterLap
  • NumPy
  • Rich

Operating Systems

  • Linux, macOS, and Windows 10 Subsystem for Linux.


To run SPLICE-q with default parameters, it requires a BAM file and a genome annotation file provided by GENCODE or Ensembl (GTF):

$ -b file.bam -g annotation.gtf

To specify an output file name and location:

$ -b file.bam -g annotation.gtf -o outfile.tsv

Need help?

$ -h

or check our User Manual.



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