ArticleBMC research notes2010
MethVisual - visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing.
Article in BMC research notes, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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
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
11 citing papers in PubMed.
- M2Viz: a tool for visualizing genetic or proteomic modifications and variants.BMC bioinformatics · 2026Article
- Filtering High-Dimensional Methylation Marks With Extremely Small Sample Size: An Application to Gastric Cancer Data.Frontiers in genetics · 2021Article
- Targeted expression profiling reveals distinct stages of early canine fibroblast reprogramming are regulated by 2-oxoglutarate hydroxylases.Stem cell research & therapy · 2020Article
- Purity estimation from differentially methylated sites using Illumina Infinium methylation microarray data.Cell cycle (Georgetown, Tex.) · 2020Article
- NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule.Scientific reports · 2019Article
- Inhibition of coiled coil domain containing protein 69 enhances platinum-induced apoptosis in ovarian cancer cells.Oncotarget · 2017Article
- Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children's Environmental Health Studies: The Children's Environmental Health and Disease Prevention Research Center's Epigenetics Working Group.Environmental health perspectives · 2017Article
- CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13-gene panel.Clinical epigenetics · 2017Article
- Identification of differentially methylated loci using wavelet-based functional mixed models.Bioinformatics (Oxford, England) · 2016Article
- MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing.BMC bioinformatics · 2016Article
- Review of processing and analysis methods for DNA methylation array data.British journal of cancer · 2013Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundExploration of DNA methylation and its impact on various regulatory mechanisms has become a very active field of research. Simultaneously there is an arising need for tools to process and analyse the data together with statistical investigation and visualisation.
findingsMethVisual is a new application that enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. The package allows the import of DNA methylation sequences, aligns them and performs quality control comparison. It comprises basic analysis steps as lollipop visualization, co-occurrence display of methylation of neighbouring and distant CpG sites, summary statistics on methylation status, clustering and correspondence analysis. The package has been developed for methylation data but can be also used for other data types for which binary coding can be inferred. The application of the package, as well as a comparison to existing DNA methylation analysis tools and its workflow based on two datasets is presented in this paper.
conclusionsThe R package MethVisual offers various analysis procedures for data that can be binarized, in particular for bisulfite sequenced methylation data. R/Bioconductor has become one of the most important environments for statistical analysis of various types of biological and medical data. Therefore, any data analysis within R that allows the integration of various data types as provided from different technological platforms is convenient. It is the first and so far the only specific package for DNA methylation analysis, in particular for bisulfite sequenced data available in R/Bioconductor enviroment. The package is available for free at http://methvisual.molgen.mpg.de/ and from the Bioconductor Consortium http://www.bioconductor.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.