txtools use cases omic references and processed data

Dataset This dataset entry is meant to be downloaded programmatically while rendering the txtools_useCases.Rmd notebooks, to facilitate their replication using the provided genomic references. Processed data is also provided to show ready-to-use examples of data processed by txtools. Abstract We present txtools, an R package that enables the processing, analysis, and visualization of RNA-seq data at the nucleotide-level resolution, seamlessly integrating alignments to the genome with transcriptomic representation. txtools’ main inputs are BAM files and a transcriptome annotation, and the main output is a table, capturing mismatches, deletions, and the number of reads beginning and ending at each nucleotide in the transcriptomic space. txtools further facilitates downstream visualization and analyses. We showcase, using examples from the epitranscriptomic field, how a few calls to txtools functions can yield insightful and ready-to-publish results. txtools is of broad utility also in the context of structural mapping and RNA:protein interaction mapping. By providing a simple and intuitive framework, we believe that txtools will be a useful and convenient tool and pave the path for future discovery. txtools is available for installation from its GitHub repository at https://github.com/AngelCampos/txtools.数据集 本数据集条目旨在于运行txtools_useCases.Rmd笔记时以编程方式下载，以便借助提供的基因组参考资料复现相关分析流程。同时还提供了已处理数据，用以展示经txtools处理后的可用实例。 摘要 我们推出了txtools：一款可在核苷酸分辨率水平处理、分析并可视化RNA测序（RNA-seq）数据的R软件包，能够将基因组比对结果与转录组表征无缝整合。txtools的主要输入为BAM文件与转录组注释文件，核心输出则是一张表格，可记录转录组空间中每个核苷酸位点的错配、缺失情况，以及起始和终止于该位点的测序读段数量。txtools还可进一步支持下游可视化与分析工作。我们以表观转录组学领域的实例为演示，展示仅需少量txtools函数调用即可获得具有洞察价值且可直接用于发表的分析结果。此外，txtools在RNA结构映射与RNA-蛋白质相互作用映射领域同样具有广泛应用价值。凭借简洁直观的框架设计，我们相信txtools将成为一款实用便捷的工具，并为后续科研发现铺平道路。用户可通过其GitHub仓库（https://github.com/AngelCampos/txtools）安装txtools。