ArticleBMC bioinformatics2017
GSAR: Bioconductor package for Gene Set analysis in R.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Ticagrelor inhibits platelet aggregation and reduces inflammatory burden more than clopidogrel in patients with stages 4 or 5 chronic kidney disease.Vascular pharmacology · 2023Trial
- Weighted overlapping group lasso for integrating prior network knowledge into gene set analysis.BMC bioinformatics · 2025Article
- Plasma proteomics for biomarker discovery in childhood tuberculosis.Nature communications · 2025Article
- Host-Associated Genetic Differentiation in the Face of Ongoing Gene Flow: Ecological Speciation in a Pathogenic Parasite of Freshwater Fish.Molecular biology and evolution · 2025Article
- Improving data interpretability with new differential sample variance gene set tests.BMC bioinformatics · 2025Article
- DNA Electrotransfer Regulates Molecular Functions in Skeletal Muscle.Bioelectricity · 2024Review
- Group B Streptococcus Drives Major Transcriptomic Changes in the Colonic Epithelium.Infection and immunity · 2023Article
- Transcriptomic Analysis of the Acute Skeletal Muscle Effects after Intramuscular DNA Electroporation Reveals Inflammatory Signaling.Vaccines · 2022Article
- GSA Central-A web platform to perform, learn, and discuss gene set analysis.Frontiers in medicine · 2022Article
- Resistant starch slows the progression of CKD in the 5/6 nephrectomy mouse model.Physiological reports · 2020Article
- Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges.Entropy (Basel, Switzerland) · 2020Review
- Article
- L1000 Viewer: A Search Engine and Web Interface for the LINCS Data Repository.Frontiers in genetics · 2019Article
- RNA-Sequencing of Umbilical Cord Blood to Investigate Spontaneous Preterm Birth: A Pilot Study.AJP reports · 2019Article
- Altered expression of K13 disrupts DNA replication and repair in Plasmodium falciparum.BMC genomics · 2018Article
- DiffGRN: differential gene regulatory network analysis.International journal of data mining and bioinformatics · 2018Article
- Identification of Crucial Genes and Pathways in Human Arrhythmogenic Right Ventricular Cardiomyopathy by Coexpression Analysis.Frontiers in physiology · 2018Article
- Platform-independent gene expression signature differentiates sessile serrated adenomas/polyps and hyperplastic polyps of the colon.BMC medical genomics · 2017Article
- Psychiatric polygenic risk associates with cortical morphology and functional organization in aging.Translational psychiatry · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundGene set analysis (in a form of functionally related genes or pathways) has become the method of choice for analyzing omics data in general and gene expression data in particular. There are many statistical methods that either summarize gene-level statistics for a gene set or apply a multivariate statistic that accounts for intergene correlations. Most available methods detect complex departures from the null hypothesis but lack the ability to identify the specific alternative hypothesis that rejects the null.
resultsGSAR (Gene Set Analysis in R) is an open-source R/Bioconductor software package for gene set analysis (GSA). It implements self-contained multivariate non-parametric statistical methods testing a complex null hypothesis against specific alternatives, such as differences in mean (shift), variance (scale), or net correlation structure. The package also provides a graphical visualization tool, based on the union of two minimum spanning trees, for correlation networks to examine the change in the correlation structures of a gene set between two conditions and highlight influential genes (hubs).
conclusionsPackage GSAR provides a set of multivariate non-parametric statistical methods that test a complex null hypothesis against specific alternatives. The methods in package GSAR are applicable to any type of omics data that can be represented in a matrix format. The package, with detailed instructions and examples, is freely available under the GPL (> = 2) license from the Bioconductor web site.
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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.