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parcor specifications

Information


Unique identifier OMICS_14608
Name parcor
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 0.2-6
Stability Stable
Requirements
MASS, glmnet, Epi, ppls, GeneNet
Source code URL https://cran.r-project.org/src/contrib/parcor_0.2-6.tar.gz
Maintained Yes

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Documentation


Maintainer


  • person_outline Nicole Kraemer

Publication for parcor

parcor citations

 (5)
library_books

Identifying the Prognosis Factors in Death after Liver Transplantation via Adaptive LASSO in Iran

2016
PMCID: 5014976
PMID: 27648080
DOI: 10.1155/2016/7620157

[…] low risk patients was then compared by calculating the areas under the curve (AUC) in receiver operating characteristic (ROC) curve. Statistical analysis was performed using SPSS 20.0, MedCalc 14.0, parcor and ridge packages in R 3.1.3 software. […]

library_books

Discovering gene re ranking efficiency and conserved gene gene relationships derived from gene co expression network analysis on breast cancer data

2016
Sci Rep
PMCID: 4759568
PMID: 26892392
DOI: 10.1038/srep20518

[…] ghbors distances. MRNETB is implemented in MINET (Mutual Information NETworks) R-package. C3net is included in the homonym R-package C3NET. Lasso and Adaptive lasso regression methods are included in PARCOR R-package which estimates the matrix of partial correlations based on different regularized regression methods. GeneNet and WGCNA are included in ENA (Ensemble network aggregation) R-package wh […]

library_books

Machine Learning Methods Enable Predictive Modeling of Antibody Feature:Function Relationships in RV144 Vaccinees

2015
PLoS Comput Biol
PMCID: 4395155
PMID: 25874406
DOI: 10.1371/journal.pcbi.1004185

[…] Lars [,], Gaussian Process Regression (GP) [], and Support Vector Regression (SVR) []. Lars performs penalized linear regression with the L1-norm lasso penalty discussed above for PLR. The R package “parcor” was used for Lars. As with PLR the penalty weight was selected by cross-validation. The parameter for the number of splits was set to 10 for robust fitting. GP performs nonlinear regression ba […]

library_books

Graph Constrained Discriminant Analysis: A New Method for the Integration of a Graph into a Classification Process

2011
PLoS One
PMCID: 3195079
PMID: 22022543
DOI: 10.1371/journal.pone.0026146

[…] reARACNE , a method based on the computation of mutual information, implemented in the package minet ,ridge.net , based on the estimation of the partial correlation matrix, implemented in the package parcor ,and the KEGG pathway hsa05200, that pertains to the biological samples we considered. The network was extracted thanks to the Bioconductor library KEGGgraph .For the two first kinds of GRN men […]

library_books

Gene Expression Network Reconstruction by Convex Feature Selection when Incorporating Genetic Perturbations

2010
PLoS Comput Biol
PMCID: 2996324
PMID: 21152011
DOI: 10.1371/journal.pcbi.1001014

[…] Step 2 of the algorithm, the lasso problems from Equation (2) and (3) are solved using the cyclic coordinate descent method of Friedman et al. , as implemented in the ‘glmnet’ package, called by the ‘parcor’ package . While this method is an approximation to solving the adaptive lasso for the log-likelihood defined in Equation (4), there are theoretical connections between an exact solution to the […]

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parcor institution(s)
Machine Learning/Intelligent Data Analysis Group, Berlin Institute of Technology, Berlin, Germany; Seminar für Statistik, ETH Zurich, Zurich, Switzerland; Basel Institute for Clinical Epidemiology and Biostatistics, University Hospital Basel, Basel, Switzerland; Department of Statistics, University of Munich, Munich, Germany; Computational Molecular Medicine Research Group, Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Germany
parcor funding source(s)
This work was supported by the BMBF grant FKZ 01-IS07007A (ReMind), the FP7-ICT Programme of the European Community, under the PASCAL2 Network of Excellence, ICT-216886, by DSM Nutritional Products Ltd. (Basel, Switzerland) and by the LMU-innovativ Project BioMed-S: Analysis and Modelling of Complex Systems in Biology and Medicine.

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