ArticleBMC bioinformatics2011
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
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- Clinical, pathological and gene expression profiling of estrogen receptor discordance in breast cancer.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2025Article
- Disease-driven restructuring of the gut microbiome underlies inflammatory bowel disease dysbiosis.Frontiers in microbiology · 2025Article
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- New insights into COL26A1 in thyroid carcinoma: prognostic prediction, functional characterization, immunological drug target and ceRNA network.Translational cancer research · 2023Article
- Analysis of asymptomatic Drosophila models for ALS and SMA reveals convergent impact on functional protein complexes linked to neuro-muscular degeneration.BMC genomics · 2023Article
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- Genomic Insights Into the Mechanism of Carbapenem Resistance Dissemination in Enterobacterales From a Tertiary Public Heath Setting in South Asia.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2023Article
- Decreased expression ofFrontiers in oncology · 2023Article
- TMUB1 expression is associated with the prognosis of colon cancer and immune cell infiltration.PeerJ · 2023Article
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- Expression characteristic, immune signature, and prognosis value of EFNA family identified by multi-omics integrative analysis in pan-cancer.BMC cancer · 2022Article
- Dissecting the ferroptosis-related prognostic biomarker and immune microenvironment of driver gene-negative lung cancer.Experimental biology and medicine (Maywood, N.J.) · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe iRefIndex addresses the need to consolidate protein interaction data into a single uniform data resource. iRefR provides the user with access to this data source from an R environment.
resultsThe iRefR package includes tools for selecting specific subsets of interest from the iRefIndex by criteria such as organism, source database, experimental method, protein accessions and publication identifier. Data may be converted between three representations (MITAB, edgeList and graph) for use with other R packages such as igraph, graph and RBGL.The user may choose between different methods for resolving redundancies in interaction data and how n-ary data is represented. In addition, we describe a function to identify binary interaction records that possibly represent protein complexes. We show that the user choice of data selection, redundancy resolution and n-ary data representation all have an impact on graphical analysis.
conclusionsThe package allows the user to control how these issues are dealt with and communicate them via an R-script written using the iRefR package - this will facilitate communication of methods, reproducibility of network analyses and further modification and comparison of methods by researchers.
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What OpenQuestion holds
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.