ArticleBioinformatics (Oxford, England)2023
Efficient querying of genomic reference databases with gget.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- Mapping the transcriptional diversity of calcium signaling in the mouse and human brain.iScience · 2026Article
- Resolving thyroid lineage cell trajectories merging into a dual endocrine gland in mammals.Nature communications · 2026Article
- Dependence of cell fate potential and cadherin switching on the coordinate within the primitive streak during differentiation of human pluripotent stem cells.Development (Cambridge, England) · 2026Article
- Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.Nature neuroscience · 2026Article
- Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes.Nature biotechnology · 2026Article
- Residual allelic activity likely underlies the low rates of disease expression for predicted loss-of-function variants in population-scale biobanks.American journal of human genetics · 2025Article
- Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes.bioRxiv : the preprint server for biology · 2025Article
- Heterogeneous constraint and adaptation across the malaria parasite life cycle.Proceedings. Biological sciences · 2025Article
- Automatic biomarker discovery and enrichment with BRAD.Bioinformatics (Oxford, England) · 2025Article
- kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq.Nature protocols · 2025Review
- Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression.bioRxiv : the preprint server for biology · 2025Article
- Resilience of A Learned Motor Behavior After Chronic Disruption of Inhibitory Circuits.bioRxiv : the preprint server for biology · 2024Article
- The impact of package selection and versioning on single-cell RNA-seq analysis.bioRxiv : the preprint server for biology · 2024Article
- Fast and scalable querying of eukaryotic linear motifs with gget elm.Bioinformatics (Oxford, England) · 2024Article
- kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.bioRxiv : the preprint server for biology · 2024Article
- AnoPrimer: Primer Design in malaria vectors informed by range-wide genomic variation.Wellcome open research · 2024Article
- AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins' Topology.Molecules (Basel, Switzerland) · 2023Article
- Generation and molecular characterization of human pluripotent stem cell-derived pharyngeal foregut endoderm.Developmental cell · 2023Article
- Genetic determinants of host tropism in Klebsiella phages.Cell reports · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
motivationA recurring challenge in interpreting genomic data is the assessment of results in the context of existing reference databases. With the increasing number of command line and Python users, there is a need for tools implementing automated, easy programmatic access to curated reference information stored in a diverse collection of large, public genomic databases.
resultsgget is a free and open-source command line tool and Python package that enables efficient querying of genomic reference databases, such as Ensembl. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying required for genomic data analysis in a single line of code. AVAILABILITY AND IMPLEMENTATION: The manual and source code are available at https://github.com/pachterlab/gget. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.