CINdex specifications


Unique identifier OMICS_15290
Name CINdex
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Segmentation data
Output data CIN values.
Output format TXT, CSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.8.0
First release date 2016
Stability Stable
methods, stats, gplots, graphics, BiocGenerics, IRanges, GenomicRanges, utils, testthat, S4Vectors, GenomeInfoDb, Biostrings, rtracklayer, grDevices, dplyr, RUnit, R(>=3.3), knitr,, biovizBase, AnnotationHub, stringr, som, gridExtra, pd.genomewidesnp.6, png, bitops, Homo.sapiens, ReactomePA, TxDb.Hsapiens.UCSC.hg18.knownGene
Maintained Yes


  • Primates
    • Homo sapiens



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CINdex in publications

PMCID: 5902833
PMID: 29665813
DOI: 10.1186/s12944-018-0739-z

[…] widely applied in clinical settings. more recent indices, including the visceral adiposity index (vai), the lipid accumulation product (lap), the abdominal volume index (avi) and the conicity index (cindex), which are calculated on the basis of simple data such as triglycerides (tg), high-density lipoprotein (hdl), body mass index (bmi), weight, height, wc, and hip circumference (hc), have also […]

PMCID: 5870913
PMID: 29580215
DOI: 10.1186/s12885-018-4240-x

[…] included. os and pfs were evaluated by the kaplan-meier method. two nomograms for predicting os and pfs were established, and the predictive accuracy was measured by the concordance index (cindex) and calibration plots., lymph node ratio (lnr), carbohydrate antigen 19–9 (ca19–9) and anatomical location were incorporated into the nomogram for os prediction and lnr, ca19–9; anatomical […]

PMCID: 5798191
PMID: 29402330
DOI: 10.1186/s12933-018-0669-0

[…] g. 1 fig. 2 fig. 3 table 2aadjustment for: age, gender, bmi, hypertension, hyperlipidemia, creatinine level and smokingbacute coronary syndrome (n = 6576) versus non acute coronary syndrome (n = 5844)cindex procedure: (a) diagnostic catheterization (no revascularization), (b) cabg, (c) pci fig. 4, aadjustment for: age, gender, bmi, hypertension, hyperlipidemia, creatinine level and smoking, bacute […]

PMCID: 5646852
PMID: 29045466
DOI: 10.1371/journal.pone.0186665

[…] of 0.05 was used. a concordance index (c index) was estimated for each right censored survival time fitted, by applying fine and gray competing risks models, and assessed at 48 months. the function cindex, implemented in the library pec, was used to estimates c indexes for each fitted model. c indexes were used to measure and compare the discriminative power of risk prediction models taking […]

PMCID: 5643429
PMID: 29038455
DOI: 10.1038/s41598-017-13448-3

[…] algorithms included the following non-parametric models: (i) the cox model, the net-cox method with lasso and elastic-net regularisation; (ii) models based on boosting trees (bt): bt-cox, bt-cindex; (iii) boosting gradient linear models (bglm): bglm-cox, bglm-cindex; and (iv) random forest based methods: random survival forest (rsf), random forest using maximally selected rank statistics […]

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CINdex institution(s)
Georgetown University, MD, USA

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