ArticlePloS one2011
SNPpy--database management for SNP data from genome wide association studies.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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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
6 citing papers in PubMed.
- Big Data in Gastroenterology Research.International journal of molecular sciences · 2023Review
- A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data.Database : the journal of biological databases and curation · 2021Article
- Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.PloS one · 2021Article
- dbVOR: a database system for importing pedigree, phenotype and genotype data and exporting selected subsets.BMC bioinformatics · 2015Article
- Next generation distributed computing for cancer research.Cancer informatics · 2014Review
- snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing.BMC bioinformatics · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundWe describe SNPpy, a hybrid script database system using the Python SQLAlchemy library coupled with the PostgreSQL database to manage genotype data from Genome-Wide Association Studies (GWAS). This system makes it possible to merge study data with HapMap data and merge across studies for meta-analyses, including data filtering based on the values of phenotype and Single-Nucleotide Polymorphism (SNP) data. SNPpy and its dependencies are open source software.
resultsThe current version of SNPpy offers utility functions to import genotype and annotation data from two commercial platforms. We use these to import data from two GWAS studies and the HapMap Project. We then export these individual datasets to standard data format files that can be imported into statistical software for downstream analyses.
conclusionsBy leveraging the power of relational databases, SNPpy offers integrated management and manipulation of genotype and phenotype data from GWAS studies. The analysis of these studies requires merging across GWAS datasets as well as patient and marker selection. To this end, SNPpy enables the user to filter the data and output the results as standardized GWAS file formats. It does low level and flexible data validation, including validation of patient data. SNPpy is a practical and extensible solution for investigators who seek to deploy central management of their GWAS data.
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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.