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Protocols

CINdex specifications

Information


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
Requirements
methods, stats, gplots, graphics, BiocGenerics, IRanges, GenomicRanges, utils, testthat, S4Vectors, GenomeInfoDb, Biostrings, rtracklayer, grDevices, dplyr, RUnit, R(>=3.3), knitr, org.Hs.eg.db, biovizBase, AnnotationHub, stringr, som, gridExtra, pd.genomewidesnp.6, png, bitops, Homo.sapiens, ReactomePA, TxDb.Hsapiens.UCSC.hg18.knownGene
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

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Documentation


Maintainer


CINdex citations

 (19)
call_split

Neck circumference as an independent indicator of visceral obesity in a Chinese population

2018
PMCID: 5902833
PMID: 29665813
DOI: 10.1186/s12944-018-0739-z
call_split See protocol

[…] ed as the weight in kilograms divided by the height in meters squared. WHR and WHtR were calculated as waist circumference divided by hip circumference and height, respectively. The VAI, LAP, AVI and Cindex were calculated as follows [, ]:Males:VAI=WCcm/39.68+1.88×BMIkg/m2×TGmmol/L/1.03×1.31/HDLmmol/LLAP=WCcm–65×TGmmol/LFemales:VAI=WCcm/36.58+1.89×BMIkg/m2×TGmmol/L/0.81×1.52/HDLmmol/LLAP=WCcm–58×T […]

library_books

CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data

2017
Cancer Inform
PMCID: 5761903
PMID: 29343938
DOI: 10.1177/1176935117746637

[…] ges with segmentation algorithms is that the segments are unique to each patient, which complicates a global analysis of the segment data in a group of patients.We have created a Bioconductor package—CINdex—that can perform a global analysis of the segment data in a group of patients. The CINdex Bioconductor package accepts the segment information from any segmentation algorithm. It calculates a n […]

library_books

Factors predicting cardiovascular events in chronic kidney disease patients. Role of subclinical atheromatosis extent assessed by vascular ultrasound

2017
PLoS One
PMCID: 5646852
PMID: 29045466
DOI: 10.1371/journal.pone.0186665

[…] l 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 into […]

library_books

A comparative study of machine learning methods for time to event survival data for radiomics risk modelling

2017
Sci Rep
PMCID: 5643429
PMID: 29038455
DOI: 10.1038/s41598-017-13448-3

[…] ithms achieved in general a high prognostic performance on the validation cohort. The best single performances were obtained by the MSR-RF (C-Index: 0.71, 95% confidence interval [0.62–0.83]), the BT-CIndex (C-Index: 0.71, [0.62–0.82]), the BT-Weibull (C-Index: 0.70, [0.60–0.82]) and the BT-COX (C-Index: 0.70, [0.59–0.81]) algorithms, all in combination with the Spearman feature selection method.F […]

library_books

An Adaptive Trajectory Clustering Method Based on Grid and Density in Mobile Pattern Analysis

2017
PMCID: 5621022
PMID: 28869503
DOI: 10.3390/s17092013

[…] ndex,j)>θthreshold then4:   pj is added into the set TRc5:   index=j; j=j+1;6: pend=pn;7: pend is added into the set TRc// trajectory partition phase8: index =1; 9: for j=2 to m in the TRc10:  if MDL(cindex,cj)>LD(cindex,cj)11:    TScindex−cj is a discrete representative trajectory segment, and added into the set DTS12:    index=j; j=j+1;13: end for14: return the set DTS.As shown in lines 1 to 7 o […]

library_books

An Update on Statistical Boosting in Biomedicine

2017
PMCID: 5558647
PMID: 28831290
DOI: 10.1155/2017/6083072

[…] st notably, the development of the package is now hosted entirely on github in the collaborative project boost-R/mboost and the package maintainer changed.The mboost 2.7 version provides a new family Cindex [], variable importance measures (varimp), and improved plotting facilities.The current CRAN version mboost 2.8 includes major changes to the Binomial family which now additionally provides an […]

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CINdex institution(s)
Georgetown University, MD, USA

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