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Protocols

MethLAB specifications

Information


Unique identifier OMICS_00797
Name MethLAB
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data The phenotype file, the methylation file, and the annotation file.
Input format TXT or CSV
Output data A text file that contains the t-statistics, p-values and flags indicating the Bonferroni/Holm significance and FDR significance of each CpG site for a given model, Q-Q Plots, Manhattan Plot, plots of individual CpG sites and a log file.
Operating system Unix/Linux
Programming languages R
Computer skills Medium
Version 2.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Karen N. Conneely
  • person_outline Varun Kilaru

Publication for MethLAB

library_books

MethLAB

2012 Epigenetics
PMCID: 3335946
PMID: 22430798
DOI: 10.4161/epi.7.3.19284

MethLAB citations

 (10)
library_books

Effects of maternal obesity on Wharton’s Jelly mesenchymal stromal cells

2017
Sci Rep
PMCID: 5730612
PMID: 29242640
DOI: 10.1038/s41598-017-18034-1

[…] ut. In addition, probes having a detection p-value above 0.01 were filtered out, and 1921 probes were thus removed from analysis. The remaining 483591 probes were analysed. The CpGassoc R package and Methlab software were used for differential methylation analysis together with the HumanMethylation450 v1.2 Manifest File containing CpG annotations. T-statistics were calculated using logit transform […]

library_books

DNA methylation analysis of paediatric low grade astrocytomas identifies a tumour specific hypomethylation signature in pilocytic astrocytomas

2016
PMCID: 4882864
PMID: 27229157
DOI: 10.1186/s40478-016-0323-6

[…] Differential methylation analysis was performed using the MethLAB R-based programme [] (R version 2.15.0). The programme enables us to identify significantly differentially methylated CpGs from the corrected β-values. The linear model with the factor of inte […]

library_books

Ethnicity and Smoking Associated DNA Methylation Changes at HIV Co Receptor GPR15

2015
PMCID: 4585036
PMID: 26441693
DOI: 10.3389/fpsyt.2015.00132

[…] ed using the Illumina Genome Studio Methylation Module Version 3.2, and values with a detection p-value greater than 0.05 were removed using a PERL script.The genome-wide data were analyzed using the MethLAB Version 1.5 (), an R package, as previously described (). Smoking-related differential methylation between smokers and non-smokers was assessed while controlling for ethnicity, slide, and plat […]

library_books

Higher levels of protective parenting are associated with better young adult health: exploration of mediation through epigenetic influences on pro inflammatory processes

2015
Front Psychol
PMCID: 4446530
PMID: 26074840
DOI: 10.3389/fpsyg.2015.00676

[…] D8+ T cells, CD14+ monocytes, CD19+ B cells, and CD56+ Natural Killer cells) using data contributed by (; GEO database under accession number GSE35069) and analyses were performed using regression in MethLAB, Version 1.5 (). The 100 sites best differentiating to the five cell types of interest were retained for further analysis in SPSS version 22 (). A locus determined to be on the X chromosome wa […]

library_books

Aberrant methylation of ERBB pathway genes in sporadic colorectal cancer

2014
J Appl Genet
PMCID: 4412553
PMID: 25366420
DOI: 10.1007/s13353-014-0253-6

[…] Linear regression was used to assess differential methylation from HM27 data using MethLAB software (Kilaru et al. ). All p-values were corrected using Benjamini–Hochberg (B-H) false discovery rate correction. All probes with difference in β-values ≥0.20 and significant B-H-correcte […]

call_split

Gene Specific Differential DNA Methylation and Chronic Arsenic Exposure in an Epigenome Wide Association Study of Adults in Bangladesh

2014
Environ Health Perspect
PMCID: 4286273
PMID: 25325195
DOI: 10.1289/ehp.1307884
call_split See protocol

[…] onducted a lookup of individual CpG loci of interest within our data set. For these analyses a CpG locus associated with p < 0.05 was considered to be statistically significant. We used the R program MethLAB v1.5 () and SAS software (SAS Institute Inc., Cary, NC, USA) to run all analyses. […]

Citations

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MethLAB institution(s)
Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA; Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA; Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA; Department of Human Genetics, Emory University, Atlanta, GA, USA
MethLAB funding source(s)
Supported in part by the National Institute of Mental Health (MH088609 and MH085806).

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