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pensim specifications


Unique identifier OMICS_15886
Name pensim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.2.9
Stability Stable
parallel, MASS, survival, penalized, survivalROC, R(≥2.10.0)
Source code URL
Maintained Yes


No version available



  • person_outline Igor Jurisica <>

Publication for pensim

pensim citations


Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites

PMCID: 5140048
PMID: 27923063
DOI: 10.1371/journal.pcbi.1005198

[…] is the regression coefficient for the kth rbp of mrna j. this model was fitted by maximum penalized likelihood with ridge or lasso penalty applied to rbps but not to mrna measurements, using the pensim r package [], which acts as a wrapper providing nested cross-validation to the penalized r package []. in the nested cross-validation scheme, test samples are held out for accuracy estimation […]


A 19 Gene expression signature as a predictor of survival in colorectal cancer

PMCID: 5016995
PMID: 27609023
DOI: 10.1186/s12920-016-0218-1

[…] 2d optimization of the penalties. the penalty parameters were tuned 50 times using different folding of the data for calculating cvl, and the penalty parameters with maximum cvl were selected by pensim r package, available at, we performed the elastic net [] using the opt2d function of the “pensim” r package to predict the survival […]


Application of Penalized Regression Techniques in Modelling Insulin Sensitivity by Correlated Metabolic Parameters

PMCID: 4636325
PMID: 26544569
DOI: 10.1371/journal.pone.0141524

[…] of degrees of freedom used for the penalty and result thus in aic or bic, respectively []. variable shrinkage (ridge, lasso, enet 1 and enet 2) was performed using the “penalized” package [, ]. the “pensim” package was used for simultaneous optimization of λ 1 and λ 2 (enet 3) []. the shrinkage parameters were assessed by 10-fold cross validation., all simulations were performed according […]


Review and evaluation of penalised regression methods for risk prediction in low‐dimensional data with few events

PMCID: 4982098
PMID: 26514699
DOI: 10.1002/sim.6782

[…] studies, and more recently by efron ., all the analyses and simulations were carried out in r. we used the package ‘glmnet’ to fit models using ridge, lasso and adaptive lasso and the packages ‘pensim’ for elastic net and ‘ncvreg’ for scad. the tuning parameters were selected using 10‐fold cross‐validation. for bayesian methods, we used jags to compile the models and obtained the samples […]

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pensim funding source(s)
Supported by National Science Foundation grant (NSF DBI-1053486); Canada Foundation for Innovation (CFI #12301 and CFI #203383) and Ontario Research Fund (GL2-01-030) supporting computational analysis, partially; Canada Research Chair Program; Ontario Ministry of Health and Long Term Care.

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