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MMBGX specifications

Information


Unique identifier OMICS_07624
Name MMBGX
Alternative name Multi-Mapping Bayesian Gene eXpression
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 0.99.26
Stability Stable
Requirements
annmap, oligo, inline, Rcpp
Maintained Yes

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Maintainer


  • person_outline Ernest Turro <>

Publication for Multi-Mapping Bayesian Gene eXpression

MMBGX in publications

 (6)
PMCID: 5444266
PMID: 26944083
DOI: 10.1093/bib/bbw016

[…] raw abundance estimates, suggesting that fold change normalization against a control is an important step for integrating expression data across platforms. based on rt-qpcr validations, express and multi-mapping bayesian gene expression (mmbgx) programs achieved the best performance for rna-seq and exon-array platforms, respectively, for deriving the isoform-level fold change values. […]

PMCID: 4652565
PMID: 26576613
DOI: 10.1186/1471-2164-16-S11-S3

[…] samples and 10 normal brain samples from tcga data portal (https://tcga-data.nci.nih.gov/tcga/); obtained the isoform expression of 114,930 transcript variants (equivalent to 35,612 genes) using the multi-mapping bayesian gene expression program []. the estimated expression values were then normalized across the samples, using the locally weighted scatterplot smoothing algorithm [], […]

PMCID: 4005667
PMID: 24503249
DOI: 10.1093/nar/gku121

[…] and 10 normal brain samples (control samples) from the tcga data portal (https://tcga-data.nci.nih.gov/tcga). the transcript (isoform)-level and gene-level expression estimates were obtained by the multi-mapping bayesian gene expression algorithm () for affymetrix whole-transcript arrays, based on ensemble database (version 56). the estimated expression values were then normalized across […]

PMCID: 3706752
PMID: 23594586
DOI: 10.1186/gm437

[…] used in this study are summarized in the supplementary information (see additional file : table s1)., the isoform level (transcript-level) and gene level expression estimates were obtained by the multi-mapping bayesian gene expression (mmbgx) algorithm for affymetrix whole-transcript arrays [], based on the ensembl database (version 56) [], which contains a total of 114,930 different […]

PMCID: 3578823
PMID: 23436997
DOI: 10.1371/journal.ppat.1003187

[…] transcribed and amplified (using the applause wt-amp plus st kit – nugen) and hybridized to affymetrix human exon 1.0st microarrays by ucl genomics. gene level analysis was performed using the mmbgx algorithm to generate gene-level data according ensembl genome annotation version 64, as mapped to the exon microarray by annmap (formerly x:map), broadly as described previously , ., […]


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MMBGX institution(s)
Department of Epidemiology and Public Health, Imperial College London, Norfolk Place, London, UK

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