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Aclust specifications

Information


Unique identifier OMICS_06081
Name Aclust
Alternative name Adjacent Site Clustering
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Tamar Sofer

Publication for Adjacent Site Clustering

Aclust citations

 (6)
library_books

Methylene tetrahydrofolate reductase contributes to allergic airway disease

2018
PLoS One
PMCID: 5766142
PMID: 29329322
DOI: 10.1371/journal.pone.0190916

[…] ere trimmed and aligned to the mouse genome mm10 using bwa-meth [] which also tabulated percent methylation at each CpG motif. Correlating sets of adjacent CpG sites were clustered together using the Adjacent Site Clustering algorithm []. Each cluster was required to have a minimum of three CpG sites to constitute a cluster. Methylation clusters were analyzed using a beta regression weighted on se […]

library_books

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

2017
Environ Health Perspect
PMCID: 5382002
PMID: 28362264
DOI: 10.1289/EHP595

[…] oothing functions, correlation structure, and/or genomic annotation, followed by drawing statistical inference on putative DMRs according to method-specific definitions. The second approach, of which aclust is the only current example, applies a clustering algorithm to reduce dimensionality prior to performing statistical tests of association.Although several DMR-finding packages exist, this field […]

library_books

Widespread DNA hypomethylation and differential gene expression in Turner syndrome

2016
Sci Rep
PMCID: 5043230
PMID: 27687697
DOI: 10.1038/srep34220

[…] moter ().After having described profound hypomethylation at the level of single CpGs, we proceeded to explore the differences in methylation between the three karyotypes at a regional level. By using adjacent site clustering, we identified 15 chrX differentially methylated regions (DMRs) and 400 autosomal DMRs (). To assess if these differences in methylation, or a lack of transcription factor exp […]

library_books

Genomic Clustering of differential DNA methylated regions (epimutations) associated with the epigenetic transgenerational inheritance of disease and phenotypic variation

2016
BMC Genomics
PMCID: 4888261
PMID: 27245821
DOI: 10.1186/s12864-016-2748-5

[…] tudies have examined clustering of specific gene families [, ]. These observations on gene clusters have been extended in a recent analysis of DNA methylation data. A novel clustering approach called adjacent site clustering (A-clustering) detects neighboring CpG sites that are correlated with methylation changes [].Previous studies by our laboratory applied a statistical clustering method to tran […]

library_books

In Utero Cigarette Smoke Affects Allergic Airway Disease But Does Not Alter the Lung Methylome

2015
PLoS One
PMCID: 4671614
PMID: 26642056
DOI: 10.1371/journal.pone.0144087

[…] thods ().Bisulfite-sequencing reads were handled using bwa-meth [] which also tabulated percent methylation at each CpG motif. Correlating sets of adjacent CpG sites were clustered together using the Adjacent Site Clustering algorithm []. Each cluster was required to have a minimum of three CpG sites to constitute a cluster. Methylation clusters were analyzed using a beta regression weighted on se […]

library_books

Multigenerational epigenetic inheritance in humans: DNA methylation changes associated with maternal exposure to lead can be transmitted to the grandchildren

2015
Sci Rep
PMCID: 4586440
PMID: 26417717
DOI: 10.1038/srep14466

[…] cific effects we CpG association analysis, which analyzes DNA methylation data using a mixed effect model at single CpG site level. For determining the Pb-dependent changes in DNA methylation we used adjacent site clustering algorithm, A-clustering to detect sets of correlated CpG sites and then tested the clusters for multivariate response to environmental exposure to Pb using the generalized est […]

Citations

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Aclust institution(s)
Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Department of Statistics, University of Connecticut, CT, USA; NIEHS, Epidemiology Branch, MD, Research Triangle Park, NC, USA; Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA

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