ArticleNucleic acids research2024
txtools: an R package facilitating analysis of RNA modifications, structures, and interactions.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed.
- Article
- Single-nucleotide m⁶A mapping uncovers redundant YTHDF function in planarian progenitor fate selection.The EMBO journal · 2026Article
- Article
- A tool for modeling gene regulatory networks (GRN_modeler) and its applications to synthetic biology.Molecular systems biology · 2025Article
- Article
- Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids.Genome biology · 2024Article
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Authors and funding
2 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.