txtools: an R package facilitating analysis of RNA modifications, structures, and interactions

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, an...

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Bibliographic Details
Published in:Nucleic acids research 2024-05, Vol.52 (8), p.e42-e42
Main Authors: Garcia-Campos, Miguel Angel, Schwartz, Schraga
Format: Article
Language:English
Subjects:
Humans
Methods
Nucleic Acid Conformation
Protein Interaction Mapping - methods
RNA - chemistry
RNA - genetics
RNA - metabolism
RNA Processing, Post-Transcriptional
RNA-Seq - methods
Sequence Analysis, RNA - methods
Software
Transcriptome
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Description
Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkae203