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charm specifications


Unique identifier OMICS_00792
Name charm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.6.0
Stability Stable
limma, methods, stats, RColorBrewer, parallel, graphics, Biobase, IRanges, utils, Biostrings, R(>=2.14.0), grDevices, BSgenome, gtools, BSgenome.Hsapiens.UCSC.hg18, preprocessCore, SQN, fields, genefilter, oligo(>=1.11.31), oligoClasses(>=1.17.39), ff, siggenes, nor1mix, sva(>=3.1.2), charmData, corpcor
Maintained Yes


No version available



  • person_outline Peter Murakami

charm citations


Functional alterations due to amino acid changes and evolutionary comparative analysis of ARPKD and ADPKD genes

Genom Data
PMCID: 5099264
PMID: 27843768
DOI: 10.1016/j.gdata.2016.10.009

[…] conditions were also integrated to the predicted protein domain structure based on the amino acid sequences of PKHD1 gene. The predicted protein domain macromolecular structure was constructed using Charm ++ and Gromacs computational programs and was studied for the stability and structural consequences compared to the mutant structure. The computational analysis is not aimed at predicting the ab […]


Efficacy and safety of dual blockade of the renin angiotensin system: meta analysis of randomised trials

PMCID: 3556933
PMID: 23358488
DOI: 10.1136/bmj.f360

[…] tly increased. Given these facts it may appropriately be asked why dual therapy was and still is extensively used to treat many patients with hypertension and heart failure. With the exception of the CHARM Added trial, most if not all data making dual therapy attractive are based on evidence from surrogate endpoints.One meta-analysis reported “encouraging” evidence that dual therapy reduced protei […]


DNA Methylation and Gene Expression Profiling of Ewing Sarcoma Primary Tumors Reveal Genes That Are Potential Targets of Epigenetic Inactivation

PMCID: 3447379
PMID: 23024594
DOI: 10.1155/2012/498472

[…] es, etc.) to identify potential therapeutic targets. Other genomewide methodologies such as Methylated CpG Island Amplification (MCA) or Comprehensive High-throughput Arrays for Relative Methylation (CHARM) have the potential to characterize the methylation profiles of more of the genome, including areas outside of the defined promoter region, such as CpG shores, which have been shown to play an i […]


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