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PGCA specifications

Information


Unique identifier OMICS_18145
Name PGCA
Alternative name Protein Group Code Algorithm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.4.0
Stability Stable
Requirements
stats, utils, testthat, knitr
Maintained Yes

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Documentation


Maintainer


  • person_outline Gabriela Cohen-Freue

PGCA citations

 (4)
library_books

PGCA: An algorithm to link protein groups created from MS/MS data

2017
PLoS One
PMCID: 5451011
PMID: 28562641
DOI: 10.1371/journal.pone.0177569

[…] trometry techniques regardless of the proteomics technology and the standard databases used. All codes were written in R (http://www.r-project.org). A library with an associated Vignette to implement PGCA algorithm is publicly available from Bioconductor (http://www.bioconductor.org). […]

library_books

Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation

2013
PLoS Comput Biol
PMCID: 3617196
PMID: 23592955
DOI: 10.1371/journal.pcbi.1002963

[…] rsion of UniProtKB database. For each analyzed sample, relative protein levels (ratios of labels 115, 116 and 117 relative to 114, respectively) were estimated for each protein group by ProteinPilot. Protein Group Code Algorithm (PGCA) was used to match protein groups identified by Protein Pilot from different experimental runs (manuscript in preparation). […]

library_books

A computational pipeline for the development of multi marker bio signature panels and ensemble classifiers

2012
BMC Bioinformatics
PMCID: 3575305
PMID: 23216969
DOI: 10.1186/1471-2105-13-326

[…] near Discriminant Analysis; SVM: Support Vector Machine; EN: Elastic Net (Generalized Linear Model); RF: Random Forest; ROC: Receiver Operating Characteristics; AUC: Area under the (ROC) Curve; PGCA: Protein Group Code Algorithm; AP: Average Probability; VT: Vote Threshold; mRNA: Messenger RNA; miRNA: MicroRNA. […]

library_books

Proteomic Signatures in Plasma during Early Acute Renal Allograft Rejection*

2010
PMCID: 2938106
PMID: 20501940
DOI: 10.1074/mcp.M110.000554

[…] ected for experimental bias using the Auto Bias correction option in the Pro Group algorithm. As the resulting protein groups may contain more than one protein identity, an in-house algorithm, called Protein Group Code Algorithm (PGCA) was used to link (local) protein groups across different iTRAQ experiments.The Protein Group Code Algorithm creates global protein groups using overlapping (or conn […]

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