ArticleGenes2020
RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow.
Article in Genes, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Transcriptional Reprogramming ofInternational journal of molecular sciences · 2026Article
- CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.BMC bioinformatics · 2026Article
- Deciphering genetic susceptibility to clear cell renal cell carcinoma.Communications biology · 2025Article
- Artificial intelligence in bioinformatics: a survey.Briefings in bioinformatics · 2025Review
- RnaXtract, a tool for extracting gene expression, variants, and cell-type composition from bulk RNA sequencing.Scientific reports · 2025Article
- Bacterial microcompartments and energy metabolism drive gut colonization by Bilophila wadsworthia.Nature communications · 2025Article
- HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets.BMC bioinformatics · 2025Article
- Article
- Delayed atorvastatin delivery promotes recovery after experimental spinal cord injury.Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2025Article
- Mucosal DNA and RNA virome alterations and their interactions with human RNA and microRNA transcriptomes in colorectal polyps.eGastroenterology · 2025Article
- Deciphering the proteome ofComputational and structural biotechnology journal · 2025Article
- TrAnnoScope: A Modular Snakemake Pipeline for Full-Length Transcriptome Analysis and Functional Annotation.Genes · 2024Article
- Erythropoiesis and Gene Expression Analysis in Erythroid Progenitor Cells Derived from Patients with Hemoglobin H/Constant Spring Disease.International journal of molecular sciences · 2024Article
- Systematic prioritization of functional variants and effector genes underlying colorectal cancer risk.Nature genetics · 2024Article
- 3t-seq: automatic gene expression analysis of single-copy genes, transposable elements, and tRNAs from RNA-seq data.Briefings in bioinformatics · 2024Article
- Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid.The Plant cell · 2024Article
- Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results.Nucleic acids research · 2024Article
- Article
- The Association between the JAK-STAT Pathway and Hypertension among Kenyan Women Diagnosed with Breast Cancer.bioRxiv : the preprint server for biology · 2024Article
- MultiRNAflow: integrated analysis of temporal RNA-seq data with multiple biological conditions.Bioinformatics (Oxford, England) · 2024Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-Seq enables the identification and quantification of RNA molecules, often with the aim of detecting differentially expressed genes (DEGs). Although RNA-Seq evolved into a standard technique, there is no universal gold standard for these data's computational analysis. On top of that, previous studies proved the irreproducibility of RNA-Seq studies. Here, we present a portable, scalable, and parallelizable Nextflow RNA-Seq pipeline to detect DEGs, which assures a high level of reproducibility. The pipeline automatically takes care of common pitfalls, such as ribosomal RNA removal and low abundance gene filtering. Apart from various visualizations for the DEG results, we incorporated downstream pathway analysis for common species as
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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.