ArticleBioinformatics (Oxford, England)2016
PaxtoolsR: pathway analysis in R using Pathway Commons.
Article in Bioinformatics (Oxford, England), 2016. 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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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
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Who cites it
19 citing papers in PubMed.
- Leveraging public AI tools to explore systems biology resources in mathematical modeling.NPJ systems biology and applications · 2025Article
- BioPAX in 2024: Where we are and where we are heading.Computational and structural biotechnology journal · 2024Review
- Medaka liver developed Human NAFLD-NASH transcriptional signatures in response to ancestral bisphenol A exposure.Research square · 2024Article
- Sex-specific expression of the human NAFLD-NASH transcriptional signatures in the liver of medaka with a history of ancestral bisphenol A exposure.bioRxiv : the preprint server for biology · 2024Article
- Robustness evaluations of pathway activity inference methods on gene expression data.BMC bioinformatics · 2024Article
- Meta-analysis of differential gene expression in lower motor neurons isolated by laser capture microdissection from post-mortem ALS spinal cords.Frontiers in genetics · 2024Article
- Article
- Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.Genome research · 2022Article
- IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis.Nucleic acids research · 2022Article
- PyBioPAX: biological pathway exchange in Python.Journal of open source software · 2022Article
- Causal interactions from proteomic profiles: Molecular data meet pathway knowledge.Patterns (New York, N.Y.) · 2021Article
- Article
- Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.Nucleic acids research · 2020Article
- Druggable Transcriptional Networks in the Human Neurogenic Epigenome.Pharmacological reviews · 2019Review
- The metaRbolomics Toolbox in Bioconductor and beyond.Metabolites · 2019Review
- ALS blood expression profiling identifies new biomarkers, patient subgroups, and evidence for neutrophilia and hypoxia.Journal of translational medicine · 2019Article
- Conserved MicroRNA Act Boldly During Sprout Development and Quality Formation in Pingyang Tezaocha (Frontiers in genetics · 2019Article
- A Landscape of Metabolic Variation across Tumor Types.Cell systems · 2018Article
- Path2enet: generation of human pathway-derived networks in an expression specific context.BMC genomics · 2016Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
purposePaxtoolsR package enables access to pathway data represented in the BioPAX format and made available through the Pathway Commons webservice for users of the R language to aid in advanced pathway analyses. Features include the extraction, merging and validation of pathway data represented in the BioPAX format. This package also provides novel pathway datasets and advanced querying features for R users through the Pathway Commons webservice allowing users to query, extract and retrieve data and integrate these data with local BioPAX datasets. AVAILABILITY AND IMPLEMENTATION: The PaxtoolsR package is compatible with versions of R 3.1.1 (and higher) on Windows, Mac OS X and Linux using Bioconductor 3.0 and is available through the Bioconductor R package repository along with source code and a tutorial vignette describing common tasks, such as data visualization and gene set enrichment analysis. Source code and documentation are at http://www.bioconductor.org/packages/paxtoolsr This plugin is free, open-source and licensed under the LGPL-3. CONTACT: paxtools@cbio.mskcc.org or lunaa@cbio.mskcc.org.
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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.