Regulatory role of the N-terminal intrinsically disordered region of the DEAD-box RNA helicase DDX3X in selective RNA recognition

This entry includes R and Python scripts and the related datasets used in the following paper."Regulatory role of the N-terminal intrinsically disordered region of human DEAD-box RNA helicase DDX3X in selective RNA recognition"Yuki Toyama, Koh Takeuchi, and Ichio Shimada<br>All of the data was uploaded as a single zip file.<br>R scriptsR 4.3.2pqsfinder_2.18.0Biostrings_2.70.2"get_transcripts_from_ensembl.R" was used to create the fasta files from the list of genes."pqsfinder.R" was used to run pqsfinder using the fasta file as an input.<br>Python scriptsPython 3.11.7numpy 1.26.3scipy 1.11.4pandas 2.1.4matplotlib 3.8.0biopython 1.78In each directory, the output files of rG4detector, pqsfinder, and G4Hunter are included in the directory named "[software]_output". These output files were created by each software using the fasta file as an input. Please refer to the manual of each software for more details. Python scripts to analyze this output data are also included. Change the transcript annotation (TEdown, TEup, concordantup, concordantdown, and mixed) in the Python script to analyze each data set. In the paper, the data from TEdown and otherwise (TEup, concordantup, concordantdown, and mixed) were compared.