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

All of the data was uploaded as a single zip file.

R scripts
R 4.3.2
pqsfinder_2.18.0
Biostrings_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.

Python scripts
Python 3.11.7
numpy 1.26.3
scipy 1.11.4
pandas 2.1.4
matplotlib 3.8.0
biopython 1.78
In 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.

本数据集包含用于以下研究论文的R、Python脚本及相关配套数据集：《人DEAD-box RNA解旋酶DDX3X的N端内在无序区域（intrinsically disordered region）在选择性RNA识别中的调控作用》（原文标题：Regulatory role of the N-terminal intrinsically disordered region of human DEAD-box RNA helicase DDX3X in selective RNA recognition），作者为Yuki Toyama、Koh Takeuchi与Ichio Shimada。所有数据已打包为单个ZIP文件上传。

### R脚本
运行环境为R 4.3.2，依赖包包括pqsfinder_2.18.0与Biostrings_2.70.2。其中`get_transcripts_from_ensembl.R`用于从基因列表生成FASTA格式文件；`pqsfinder.R`则以FASTA文件为输入运行pqsfinder工具。

### Python脚本
运行环境为Python 3.11.7，依赖库包括numpy 1.26.3、scipy 1.11.4、pandas 2.1.4、matplotlib 3.8.0、biopython 1.78。
每个子目录下的`[software]_output`文件夹中均存放rG4detector、pqsfinder及G4Hunter的输出结果文件，此类输出文件均以FASTA文件作为输入，由对应软件生成，详细使用规则请参阅各软件官方手册。本数据集同时附带用于分析上述输出数据的Python脚本，用户可修改脚本内的转录本注释标签（TEdown、TEup、concordantup、concordantdown及mixed）以适配不同数据集的分析需求。本论文中，研究人员对TEdown数据集与其余四类数据集（TEup、concordantup、concordantdown及mixed）开展了对比分析。