ArticlePeerJ2023
Seq2science: an end-to-end workflow for functional genomics analysis.
Article in PeerJ, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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.
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
16 citing papers in PubMed.
- Hypomagnesemia in Hypoparathyroidism, Sensorineural Deafness, and Renal Dysplasia Syndrome Caused by Pathogenic Variants ofKidney international reports · 2026Article
- Methylome profiling of SetDB1-deficient ESCs reveals coordinated epigenetic cross-talk during pluripotency.Stem cell reports · 2026Article
- From stem cells to somites: Revealing genetic and exogenous factors of human embryogenesis.Stem cell reports · 2026Article
- Smarcc1 drives optic stalk patterning and optic nerve head astrocyte differentiation.Development (Cambridge, England) · 2026Article
- Membrane remodelling mediates lipopeptide-induced immunity in Arabidopsis.Nature plants · 2026Article
- Persistent viral control status is associated with enhanced innate immune responses in people with HIV-1.iScience · 2026Article
- Improved flux profiling in genome-scale modeling of human cell metabolism.Cell reports methods · 2026Article
- Galectin-9 binding to HLA-DR in dendritic cells controls immune synapse formation and T cell proliferation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Double stranded RNA sensing is silenced during early embryonic development.Nature communications · 2025Article
- Phenotypic and epigenetic profiles of circulating NK cells in spontaneous HIV-1 controllers.EBioMedicine · 2025Article
- Article
- An integrated transcriptomic cell atlas of human endoderm-derived organoids.Nature genetics · 2025Article
- Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment.Stem cell reports · 2025Article
- Transcriptomic profiling of osteoarthritis synovial macrophages reveals a tolerized phenotype compounded by a weak corticosteroid response.Rheumatology (Oxford, England) · 2025Article
- Deciphering the heterogeneity of differentiating hPSC-derived corneal limbal stem cells through single-cell RNA sequencing.Stem cell reports · 2024Article
- Case Report: A severe case of immunosuppressant-refractory immune checkpoint inhibitor-mediated colitis rescued by tofacitinib.Frontiers in immunology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequencing databases contain enormous amounts of functional genomics data, making them an extensive resource for genome-scale analysis. Reanalyzing publicly available data, and integrating it with new, project-specific data sets, can be invaluable. With current technologies, genomic experiments have become feasible for virtually any species of interest. However, using and integrating this data comes with its challenges, such as standardized and reproducible analysis. Seq2science is a multi-purpose workflow that covers preprocessing, quality control, visualization, and analysis of functional genomics sequencing data. It facilitates the downloading of sequencing data from all major databases, including NCBI SRA, EBI ENA, DDBJ, GSA, and ENCODE. Furthermore, it automates the retrieval of any genome assembly available from Ensembl, NCBI, and UCSC. It has been tested on a variety of species, and includes diverse workflows such as ATAC-, RNA-, and ChIP-seq. It consists of both generic as well as advanced steps, such as differential gene expression or peak accessibility analysis and differential motif analysis. Seq2science is built on the Snakemake workflow language and thus can be run on a range of computing infrastructures. It is available at https://github.com/vanheeringen-lab/seq2science.
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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.