M3D statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool M3D
info

Tool usage distribution map

This map represents all the scientific publications referring to M3D per scientific context
info info

Associated diseases

info

Popular tool citations

chevron_left Differentially methylated region detection chevron_right
Want to access the full stats & trends on this tool?

M3D specifications

Information


Unique identifier OMICS_06803
Name M3D
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
Requirements
parallel, BiocGenerics, IRanges, GenomicRanges, testthat, S4Vectors, BiocStyle, SummarizedExperiment, Rcpp, knitr, R(>=3.3.0), BiSeq
Maintained Yes

Versioning


No version available

Documentation


Publication for M3D

M3D citations

 (5)
library_books

Integrating Epigenomics into the Understanding of Biomedical Insight

2016
Bioinform Biol Insights
PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] Seq), weighted generalized linear model (BSmooth), bump hunting with batch effect removal and peak detection (bumphunting), tunable kernel smoothing (DMR-cate), nonparametric and kernel-based method (M3D), beta-binomial model (methylSig), beta-binomial hierarchical model (MOABS), hidden Markov model (NHMMfdr), three-state HMM (MethPipe), Shannon entropy (QDMR), and a binary segmentation algorithm […]

library_books

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

2016
Front Microbiol
PMCID: 5121216
PMID: 27933038
DOI: 10.3389/fmicb.2016.01819

[…] Gene expression data were collected from the Gene Expression Omnibus (GEO) (Edgar et al., ) and M3D databases (Faith et al., ), as well as from the laboratory of Dr. Paul Dunman in the case of S. aureus. Expression data were downloaded in the form of Affymetrix GeneChip® cell intensity (CEL) fil […]

library_books

Cautions about the reliability of pairwise gene correlations based on expression data

2015
Front Microbiol
PMCID: 4481165
PMID: 26167162
DOI: 10.3389/fmicb.2015.00650

[…] able . We then combined other GSEs to create the rest of the other partial compendia.A similar approach was taken for E. coli, S. oneidensis and S. aureus. For example, E. coli data was obtained from M3D. M3D has collected data from GEO, as well as data deposited directly to M3D by other labs. To create partial compendia for E. coli we created a single partial compendium for all GEO data that is i […]

library_books

The genome scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli

2014
Nucleic Acids Res
PMCID: 4288151
PMID: 25429971
DOI: 10.1093/nar/gku1229

[…] Publicly-available gene expression (transcriptome) data for E. coli were downloaded from the M3D database (http://m3d.mssm.edu; ()). This comprises Robust Multi-array Average (RMA)-normalized gene expression measurements from Affymetrix microarrays across ∼300 conditions. Pearson correlation […]

library_books

Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

2012
BMC Bioinformatics
PMCID: 3462729
PMID: 22873695
DOI: 10.1186/1471-2105-13-193

[…] nsity (CEL) files for substantial numbers of microarray experiments. We obtained these CEL files from multiple sources: NCBI’s Gene Expression Omnibus [GEO; [], the Many Microbe Microarrays Database [M3D; [], and, in one case, a private laboratory (Dr. Paul Dunman, personal communication). Expression data from GEO and M3D is available via direct download from those repositories, while expression d […]


Want to access the full list of citations?
M3D institution(s)
IANC, School of Informatics, University of Edinburgh, Edinburgh and Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK

M3D reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review M3D