bumphunter statistics

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Citations per year

Number of citations per year for the bioinformatics software tool bumphunter
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Tool usage distribution map

This map represents all the scientific publications referring to bumphunter per scientific context
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Associated diseases

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Popular tool citations

chevron_left Differentially methylated region detection Differentially methylated region detection chevron_right
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Protocols

bumphunter specifications

Information


Unique identifier OMICS_19199
Name bumphunter
Software type Framework/Library, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.22.0
Stability Stable
Requirements
AnnotationDbi, limma, methods, stats, parallel, BiocGenerics, GenomicRanges, utils, testthat, GenomeInfoDb, locfit, RUnit, S4Vectors(>=0.9.25), GenomicFeatures, foreach, matrixStats, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, doParallel, IRanges(>=2.3.23), R(>=3.4), iterators, doRNG
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Rafael A. Irizarry

Additional information


http://bioconductor.org/packages/release/bioc/manuals/bumphunter/man/bumphunter.pdf

Publication for bumphunter

bumphunter citations

 (23)
library_books

DNA methylation modules in airway smooth muscle are associated with asthma severity

2018
PMCID: 5902304
PMID: 29449426
DOI: 10.1183/13993003.01068-2017

[…] proliferative signalling by Notch in severe asthma ASMCs.We used a different approach to examine the importance of severity associated DMPs, namely weighted gene co-expression analysis (WGCNA) [] and Bumphunter analysis []. We identified five out of 19 modules as being significantly correlated with disease severity (). Filtering of these phenotype-associated CpG sites for significance and connecti […]

library_books

Hypomethylation of CYP2E1 and DUSP22 Promoters Associated With Disease Activity and Erosive Disease Among Rheumatoid Arthritis Patients

2018
PMCID: 5876118
PMID: 29287311
DOI: 10.1002/art.40408

[…] is small . Per the regression model, P values were adjusted using the Bonferroni correction for 428,232 tests.Analysis of differentially methylated regions (DMRs) was performed as implemented in the Bumphunter R package . Coefficients from the above regression models were smoothed over genomic distance, generating candidate regions of differentially methylated CpG sites. Statistical significance […]

library_books

Genome wide DNA methylation profiling in whole blood reveals epigenetic signatures associated with migraine

2018
BMC Genomics
PMCID: 5778740
PMID: 29357833
DOI: 10.1186/s12864-018-4450-2

[…] idual CpGs were classified as hypomethylated; while, if the majority of methylation values for migraine were greater less than the controls, they were annotated as hypermethylated.We also applied the bumphunter technique [] to identify DMRs. Methylation probes were clustered so that the distance between any two probes in the same cluster was at most 1 kb. For each cluster, a linear model was fit, […]

library_books

DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty

2017
Nat Commun
PMCID: 5740109
PMID: 29269866
DOI: 10.1038/s41467-017-02326-1

[…] of the current IDU+/HCV± +group.Considering that DNA-me alterations in adjacent sites may occur together, we examined DMRs across the epigenome between HIV-infected IDU+/HCV+ and IDU−/HCV− using the BumpHunter program. A total of 148 DMRs were significantly different between groups (FDR < 0.05). We identified 19 DMRs on chromosome 6, including the region of the MHC gene clusters, i.e., HLA-H, HCG […]

library_books

The early pregnancy placenta foreshadows DNA methylation alterations of solid tumors

2017
Epigenetics
PMCID: 5739102
PMID: 28678605
DOI: 10.1080/15592294.2017.1342912

[…] and controls (e.g., chorionic villi third trimester or colon adenocarcinoma normal) were calculated for each cluster. Then, clusters within 250 kb from each other were grouped together. Finally, the Bumphunter algorithm was applied within each group to detect blocks exhibiting differences in average methylation between cases and controls. The main steps of this algorithm are the following: (i) fi […]

library_books

Exposure to Low Levels of Lead in Utero and Umbilical Cord Blood DNA Methylation in Project Viva: An Epigenome Wide Association Study

2017
Environ Health Perspect
PMCID: 5783669
PMID: 28858830
DOI: 10.1289/EHP1246

[…] f methylation values of 28 CpGs as described elsewhere (), and we adjusted for the score as a quartile-covariate instead of adjusting for the smoking status in the EWAS analyses. Finally, we used the bumphunter package from Bioconductor to perform a bumphunting analysis, as previously described (), to detect any differentially methylated regions (DMRs) relative to prenatal maternal lead exposure. […]


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bumphunter institution(s)
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health. Baltimore, MD, USA; Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
bumphunter funding source(s)
Partially supported by the National Institute of Health (grant numbers R01 GM083084, R01 RR021967, P50 HG003233; R01ES017646).

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