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


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Documentation


Maintainers


  • person_outline Karen N. Conneely <>
  • person_outline Varun Kilaru <>

Publication for MethLAB

MethLAB in publications

 (9)
PMCID: 5730612
PMID: 29242640
DOI: 10.1038/s41598-017-18034-1

[…] 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 […]

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

[…] further analysis. the dataset generated in this study has been deposited in the gene expression omnibus (geo) under accession gse77241., 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 […]

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

[…] 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, […]

PMCID: 4412553
PMID: 25366420
DOI: 10.1007/s13353-014-0253-6

[…] ii software with advanced relative quantification for all samples. all experiments were repeated in duplicate., 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 […]

PMCID: 4286273
PMID: 25325195
DOI: 10.1289/ehp.1307884

[…] 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., characteristics of the study sample are summarized in . we ran models separately for blood and urinary total […]


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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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