eNRSA: a faster and more powerful approach for nascent transcriptome analysis Article Swipe
Jing Wang
,
Hua‐Chang Chen
,
Scott W. Hiebert
,
Quanhu Sheng
,
William P. Tansey
,
Yu Shyr
,
Qi Liu
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1093/gigascience/giaf071
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1093/gigascience/giaf071
Nascent RNA sequencing tracks primary transcriptional events, making it crucial for studying the immediate regulatory changes of genes and enhancers in response to both endogenous and exogenous stimuli. NRSA is a widely used tool for analyzing nascent transcriptomic data, enabling quantification of transcriptional changes at proximal promoters and gene bodies, estimation of pausing indices, identifying active enhancers, and establishing enhancer–target gene relationships. To improve its functionality and broaden its applicability to diverse organisms and complex study designs, we have developed an enhanced version, eNRSA. Key advancements include adaptive selection of major transcripts, support for any organism with known gene structures, compatibility with complex study designs, and identification of alternative transcription start and termination sites, as well as transcription readthrough events. Additionally, eNRSA achieves a ∼20-fold increase in analysis speed while significantly reducing memory usage. These enhancements make eNRSA a faster, more versatile, and more powerful tool for nascent transcriptome analysis. eNRSA is freely available at https://bioinfo.vanderbilt.edu/eNRSA/.
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Metadata
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- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/gigascience/giaf071
- https://academic.oup.com/gigascience/article-pdf/doi/10.1093/gigascience/giaf071/63668018/giaf071.pdf
- OA Status
- gold
- References
- 59
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4412037597
All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W4412037597Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/gigascience/giaf071Digital Object Identifier
- Title
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eNRSA: a faster and more powerful approach for nascent transcriptome analysisWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-01-01Full publication date if available
- Authors
-
Jing Wang, Hua‐Chang Chen, Scott W. Hiebert, Quanhu Sheng, William P. Tansey, Yu Shyr, Qi LiuList of authors in order
- Landing page
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https://doi.org/10.1093/gigascience/giaf071Publisher landing page
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https://academic.oup.com/gigascience/article-pdf/doi/10.1093/gigascience/giaf071/63668018/giaf071.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://academic.oup.com/gigascience/article-pdf/doi/10.1093/gigascience/giaf071/63668018/giaf071.pdfDirect OA link when available
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Enhancer, Transcriptome, Computational biology, Gene, Biology, Transcription (linguistics), Transcription factor, Computer science, Genetics, Gene expression, Philosophy, LinguisticsTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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| cited_by_percentile_year | |
| countries_distinct_count | 1 |
| institutions_distinct_count | 7 |
| citation_normalized_percentile.value | 0.25076062 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |