Marmal-aid protocols

View Marmal-aid computational protocol

Marmal-aid statistics

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Marmal-aid specifications

Information


Unique identifier OMICS_00796
Name Marmal-aid
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Robert Lowe <>

Information


Unique identifier OMICS_00796
Name Marmal-aid
Interface Web user interface
Restrictions to use None
Biological technology Illumina
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Robert Lowe <>

Publication for Marmal-aid

Marmal-aid in pipelines

 (2)
2015
PMCID: 4529346
PMID: 25924914
DOI: 10.1002/cam4.451

[…] methylated in at least 40% of the tumor pairs (δβ > 0.2), were identified as the de novo methylated loci. the methylome data for pbmcs were obtained from 100 healthy females collected by the marmal-aid database ., the normalized methylome data on humanmethylation450 beadarray from eleven types of solid tumors, including prostate, breast, pancreatic, kidney, thyroid, liver, rectal, colon, […]

2015
PMCID: 4529346
PMID: 25924914
DOI: 10.1002/cam4.451

[…] beadarray from eleven types of solid tumors, including prostate, breast, pancreatic, kidney, thyroid, liver, rectal, colon, head and neck, gastric, and lung cancers, were obtained from marmal-aid database . only the samples collected in tcga studies were used in the study. limma analysis for group comparison was used to identify the differentially methylated loci in each type […]


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Marmal-aid in publications

 (21)
PMCID: 5813244
PMID: 29034560
DOI: 10.1002/gepi.22086

[…] three were taken from publicly available datasets deposited in the ncbi gene expression omnibus (http://www.ncbi.nlm.nih.gov/geo/), accessed and downloaded using the r package marmal‐aid (http://marmal-aid.org) (lowe & rakyan, ). these studies were selected as some of the largest publicly available datasets representing different ancestral populations and cell types at the time […]

PMCID: 5415776
PMID: 28473875
DOI: 10.1186/s13148-017-0344-4

[…] available for samples in the validation cohort, illumina 450k data was publically available for a number of adipose samples from lean, overweight and obese individuals. samples accessible through marmal-aid [] included those from six lean male individuals with both subcutaneous and omental adipose tissue collected at most 12 h post-mortem (gse48472 []), 14 visceral adipose (of […]

PMCID: 5391229
PMID: 28255110
DOI: 10.18632/aging.101187

[…] the strongest associations identified were for a single cpg site in myof and an extended region within the promoter of ddo. these hits were validated in curated public data from 2316 blood samples (marmal-aid). this study is the first to report robust age associations for myof and ddo, both of which have plausible functional roles in aging. this study also illustrates the value of genetic […]

PMCID: 5282868
PMID: 28163793
DOI: 10.1186/s13148-016-0303-5

[…] pathological review of representative haematoxylin and eosin (h&e) sections was conducted to include only specimens with tumour cellularity >80%. blood methylome data was retrieved from the marmal-aid database (http://marmal-aid.org, []). normal urothelium samples were taken from non-bladder cancer patients by urothelial brushings to ensure a true reflection of the normal urothelium […]

PMCID: 5234101
PMID: 28081708
DOI: 10.1186/s13059-016-1129-3

[…] spanning ~21,000 genes., to investigate the degree of leukocyte infiltration in each sample, public hm450 data from 96 male peripheral blood samples (gse53740 and gse51388) were downloaded using marmal-aid []. all hm450 probes with beta values >0.2 in male peripheral blood were excluded. the remaining probes were used to subset 500 probes that were hypermethylated in 43 tcga an prostate […]


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Marmal-aid institution(s)
The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK

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