ArticleGenome biology2021
recount3: summaries and queries for large-scale RNA-seq expression and splicing.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 184 papers.
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Who cites it
184 citing papers in PubMed, 275 citations in OpenAlex.
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- Reporting and representation of population descriptors in public RNA-seq databases.Cell genomics · 2026Article
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- Integrated inference of cellular compositions and gene expression programs by deconvolution.Cell regeneration (London, England) · 2026Article
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- Data-driven RNA phenotyping captures genetically regulated dimensions of the transcriptome.American journal of human genetics · 2026Article
- EpiATLAS - a reference for human epigenomic research.bioRxiv : the preprint server for biology · 2026Article
- Consensus Pituitary Atlas, a scalable resource for annotation, novel marker discovery, and analyses in mouse pituitary gland research.Cell reports · 2026Article
- RNA Detection Technologies: A MethodCentric Guide to Principles and Reproducibility.Bio-protocol · 2026Article
- The recount3 Python package for programmatic access to uniformly processed RNA-seq data.bioRxiv : the preprint server for biology · 2026Article
- Smoking exposure alters splicing of the nicotinic acetylcholine receptor subunit CHRNA5.Human genomics · 2026Article
- Human pancreatic progenitor organoids define genetic and epigenetic barriers to early PDAC transformation.Developmental cell · 2026Article
- Patient-specific modeling of G2/M cell cycle dynamics reveals prognostic dynamical regimes driven by copy number alterations.NPJ systems biology and applications · 2026Article
- Differential assembly of mouse and human tumor microenvironments.Nature immunology · 2026Article
- Developmental programmes drive cellular plasticity, disease progression and therapy resistance in lung adenocarcinoma.Molecular oncology · 2026Article
- The Paipu framework enables creation of a large-scale mammalian cancer transcriptomics atlas.bioRxiv : the preprint server for biology · 2026Article
- Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models.Briefings in bioinformatics · 2026Review
- Correlation of the differential expression of PIK3R1 and its spliced variant, p55α, in pan-cancer.Molecular oncology · 2026Article
- TUSCO: benchmarking transcriptome reconstruction with endogenous single-isoform controls.Nature communications · 2026Article
124 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors at 6 institutions in 2 countries.
Funding
Abstract
We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recount3 and snapcount R/Bioconductor packages as well as complementary web resources. Using these tools, data can be downloaded as study-level summaries or queried for specific exon-exon junctions, genes, samples, or other features. Monorail can be used to process local and/or private data, allowing results to be directly compared to any study in recount3. Taken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio .
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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.