ArticleNAR genomics and bioinformatics2021
pyrpipe: a Python package for RNA-Seq workflows.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- Mitochondrial OXPHOS restricts SARS-CoV-2 replication.Science advances · 2026Article
- Importance of De Novo Gene Evolution to Emerging Viral Threats: The ORF10 Strain-Restricted Orphan Gene of SARS-CoV-2 Promotes Pathogenesis.Molecular biology and evolution · 2025Article
- Quantitative spatial analysis of bacterial transcriptome and chromosome structural data with GRATIOSA: application to twin-supercoiled domain distribution.Nucleic acids research · 2025Article
- sChemNET: a deep learning framework for predicting small molecules targeting microRNA function.Nature communications · 2024Article
- Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts.Science translational medicine · 2023Article
- Article
- ARA: a flexible pipeline for automated exploration of NCBI SRA datasets.GigaScience · 2022Article
- Foster thy young: enhanced prediction of orphan genes in assembled genomes.Nucleic acids research · 2022Article
- System-wide transcriptome damage and tissue identity loss in COVID-19 patients.Cell reports. Medicine · 2022Article
- Article
- Role of miR-2392 in driving SARS-CoV-2 infection.Cell reports · 2021Article
- orfipy: a fast and flexible tool for extracting ORFs.Bioinformatics (Oxford, England) · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The availability of terabytes of RNA-Seq data and continuous emergence of new analysis tools, enable unprecedented biological insight. There is a pressing requirement for a framework that allows for fast, efficient, manageable, and reproducible RNA-Seq analysis. We have developed a Python package, (pyrpipe), that enables straightforward development of flexible, reproducible and easy-to-debug computational pipelines purely in Python, in an object-oriented manner. pyrpipe provides access to popular RNA-Seq tools, within Python, via high-level APIs. Pipelines can be customized by integrating new Python code, third-party programs, or Python libraries. Users can create checkpoints in the pipeline or integrate pyrpipe into a workflow management system, thus allowing execution on multiple computing environments, and enabling efficient resource management. pyrpipe produces detailed analysis, and benchmark reports which can be shared or included in publications. pyrpipe is implemented in Python and is compatible with Python versions 3.6 and higher. To illustrate the rich functionality of pyrpipe, we provide case studies using RNA-Seq data from GTEx, SARS-CoV-2-infected human cells, and
Identifiers
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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.