MEAP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MEAP
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Tool usage distribution map

This map represents all the scientific publications referring to MEAP per scientific context
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Associated diseases

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Popular tool citations

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Protocols

MEAP specifications

Information


Unique identifier OMICS_11341
Name MEAP
Alternative name Multiple Exon Array Preprocessing
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Parallelization MPI
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.1
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Ping Chen

Publication for Multiple Exon Array Preprocessing

MEAP citations

 (6)
library_books

Alternative splicing discriminates molecular subtypes and has prognostic impact in diffuse large B cell lymphoma

2017
PMCID: 5596382
PMID: 28841210
DOI: 10.1038/bcj.2017.71

[…] ray data are available at ArrayExpress archive (http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3488). Gene- and exon-level expression data for the NLG-LBC-04 discovery cohort were quantified by MEAP (Multiple Exon Array Preprocessing) algorithm with MEAP probe annotation version 70.In the CGCI validation cohort, adaptors and low-quality bases were trimmed from the samples before alignment. T […]

library_books

Comparative evaluation of isoform level gene expression estimation algorithms for RNA seq and exon array platforms

2016
Brief Bioinform
PMCID: 5444266
PMID: 26944083
DOI: 10.1093/bib/bbw016

[…] m abundance from exon-array data. Three such programs were tested on the TCGA exon-array data: the Multi-Mapping Bayesian Gene eXpression (MMBGX) method [], the puma R/Bioconductor package [] and the Multiple Exon Array Preprocessing (MEAP) method []. Each of these algorithms has shown better performance than two other popular tools, PILER and RMA, in their respective studies. Furthermore, these t […]

call_split

Early Maternal Alcohol Consumption Alters Hippocampal DNA Methylation, Gene Expression and Volume in a Mouse Model

2015
PLoS One
PMCID: 4430308
PMID: 25970770
DOI: 10.1371/journal.pone.0124931
call_split See protocol

[…] n the hippocampi of five control and five ethanol-exposed four-week-old male offspring (from two and three litters, respectively).The exon array probe expression values were normalized first with the MEAP algorithm [], [], [] followed by background and noise corrections. The normalized probe signals were transformed into gene expression values using MEAP. The analysis was done in the freely availa […]

library_books

The cis and trans effects of the risk variants of coronary artery disease in the Chr9p21 region

2015
BMC Med Genomics
PMCID: 4432789
PMID: 25958224
DOI: 10.1186/s12920-015-0094-0

[…] C metrics, including relative log expression (RLE), positive vs. negative ROC AUC and MAD-residual mean, were all within the parameters suggested by Affymetrix.Raw intensity data were processed using Multiple Exon Array Preprocessing (MEAP) software. The PM-BayesBG method was used for background correction. This was followed by quantile normalization, expression summarization and log2 transformati […]

library_books

Deregulation of COMMD1 Is Associated with Poor Prognosis in Diffuse Large B cell Lymphoma

2014
PLoS One
PMCID: 3953211
PMID: 24625556
DOI: 10.1371/journal.pone.0091031

[…] to genomic locus was counted. Genes with more than 10 CNVs were excluded from the subsequent analyses. Exon array expression data were normalized and transformed to gene expression level data by the Multiple Exon Array Preprocessing (MEAP) algorithm .In order to find genes with a significant association of expression and CNA, all genes in the expression data, which were located in a minimal commo […]

call_split

Functional Profiling of Precursor MicroRNAs Identifies MicroRNAs Essential for Glioma Proliferation

2013
PLoS One
PMCID: 3618426
PMID: 23577178
DOI: 10.1371/journal.pone.0060930
call_split See protocol

[…] by Anduril integration tool . Statistical analysis, Student’s T-test and log2-scale fold change, were done on level 3 microRNA expression data from TCGA and transcript expression data preprocessed by Multiple Exon Array Preprocessing (MEAP) algorithm for candidate microRNAs and their targets. Kaplan-Meier analysis was performed as described previously in Ovaska et al. , where patients were groupe […]


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MEAP institution(s)
Research Programs Unit, Genome-Scale Biology and Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, Finland; Research Programs Unit, Molecular Cancer Biology Program and Haartman Institute, University of Helsinki, Finland
MEAP funding source(s)
Academy of Finland (grant number 125826), Biocentrum Helsinki; Finnish Graduate School in Computational Sciences; the Finnish Cancer Society; Sigrid Jusélius Foundation

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