matchprobes statistics

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

This map represents all the scientific publications referring to matchprobes per scientific context
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matchprobes specifications

Information


Unique identifier OMICS_14780
Name matchprobes
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 1.14.1
Stability Stable
Requirements
Biobase, Affy
Maintained Yes

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Documentation


Maintainer


  • person_outline Wolfgang Huber

Publication for matchprobes

matchprobes citations

 (4)
library_books

Consistent annotation of gene expression arrays

2010
BMC Genomics
PMCID: 2894801
PMID: 20459806
DOI: 10.1186/1471-2164-11-294

[…] probesets to the latest genomic knowledge. For example Gautier et al have reannotated the Affymetrix HG-U133A probesets by mapping the probes against Human Refseq mRNA using the BioConductor package matchprobes [,]. Most reannotation efforts addressing GeneChip microarrays have remapped probes, or target sequences to external public databases of expressed sequence. One exception to this approach […]

library_books

Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data

2010
BMC Genomics
PMCID: 2827411
PMID: 20089164
DOI: 10.1186/1471-2164-11-50

[…] ould include more than 3 probes (see Additional File for further details). The remapped probe set definition was transformed into new probe sequence and CDF packages using the Bioconductor packages, matchprobes [] and makecdfenv []. R libraries of the probe and CDF packages, and annotation of the remapped probe sets are provided in Additional File . The probe remapping protocol is implemented in […]

library_books

SOX2 Is an Amplified Lineage Survival Oncogene in Lung and Esophageal Squamous Cell Carcinomas

2009
Nat Genet
PMCID: 2783775
PMID: 19801978
DOI: 10.1038/ng.465

[…] From existing raw expression files expression data were generated using a gene-centric CDF file. We applied RMA and quantile normalization and the matchprobes package in the Bioconductor framework to create one single data set. Only patients with pathologic stage I/II disease and less than 80 years old at diagnosis had their tumor’s expression p […]

library_books

Integrating probe level expression changes across generations of Affymetrix arrays

2005
Nucleic Acids Res
PMCID: 1316121
PMID: 16356924
DOI: 10.1093/nar/gni193

[…] e probes to mRNA sequences with BLAT, which uses heuristics to speed up the search. To evaluate the accuracy of the BLAT search, we aligned the probes of the HG-U133A array also with the Bioconductor matchprobes package, which is based on exact string matching methods. The results obtained with BLAT and matchprobes were virtually the same (BLAT missed 52 of the 241 898 unique probes). The most ess […]


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matchprobes institution(s)
Department of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany; Department of Biostatistical Science, Dana Farber Cancer Institute, Boston, MA, USA

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