Protocols

ADMIRE specifications

Information


Unique identifier OMICS_09534
Name ADMIRE
Alternative name Analysis of DNA methylation in genomic regions
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Infinium Human Methylation450K Assay
Output data Tables and graphs
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl, Python, R, Shell (Bash)
License MIT License
Computer skills Advanced
Version 1.0
Stability Stable
Requirements
comb-p, bedtools, Rscript, numpy, matplotlib
Maintained Yes

Download


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Versioning


No version available

Maintainers


  • person_outline Mario Looso
  • person_outline Jens Preussner

Additional information


http://admire.readthedocs.io/en/latest/

Information


Unique identifier OMICS_09534
Name ADMIRE
Alternative name Analysis of DNA methylation in genomic regions
Interface Web user interface
Restrictions to use None
Input data Infinium Human Methylation450K Assay
Output data Tables and graphs
Biological technology Illumina
Programming languages Perl, R
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainers


  • person_outline Mario Looso
  • person_outline Jens Preussner

Additional information


http://admire.readthedocs.io/en/latest/

Publication for Analysis of DNA methylation in genomic regions

ADMIRE citations

 (2)
library_books

Pulmonary endothelial cell DNA methylation signature in pulmonary arterial hypertension

2017
Oncotarget
PMCID: 5581088
PMID: 28881789
DOI: 10.18632/oncotarget.18031

[…] was assessed at over 485,000 CpG sites using the Illumina Infinium® HumanMethylation450 BeadChip. The slides were scanned by iScan+ (Illumina®, San Diego, USA). Raw data files were used as input for ADMIRE [], a method for analyzing DNA methylation in genomic regions. Briefly, data was quality checked and normalized using the functional normalization developed by Aryee et al. []. Two one-sided tw […]

call_split

Promoter hypermethylation as a mechanism for Lamin A/C silencing in a subset of neuroblastoma cells

2017
PLoS One
PMCID: 5397038
PMID: 28422997
DOI: 10.1371/journal.pone.0175953
call_split See protocol

[…] mas for 105 patients based on a 450K human methylation (dataset GSE73515 at gene expression omnibus https://www.ncbi.nlm.nih.gov/geo/)used in Heinrich et al study [] was downloaded and analyzed using ADMIRE [] with a customized genomic regions file, targeting only chr1:156083251-156109330(Human genome version hg19). Probes with a detection p-value larger than 0.01, as well as probes that failed in […]

ADMIRE institution(s)
Bioinformatics Group, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
ADMIRE funding source(s)
Supported by Excellence Cluster Cardio-Pulmonary System (ECCPS) and Max Planck Institute for Heart and Lung Research (MPI).

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