iCluster statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

Associated diseases

iCluster specifications

Information


Unique identifier OMICS_09010
Name iCluster
Alternative names iClusterPlus, iCluster+
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 2.1.0
Stability Stable
Requirements
gplots, parallel, lattice, gtools, caTools, gdata, R(≥2.15.0)
Maintained Yes

Versioning


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Documentation


Maintainers


  • person_outline Ronglai Shen <>
  • person_outline Qianxing Mo <>
  • person_outline Sijian Wang <>

Publications for iCluster

iCluster in publications

 (42)
PMCID: 5887505
PMID: 29529299
DOI: 10.1093/nar/gky131

[…] pathways. several methods and results have been published for the integrated analysis of multiple types of -omic data (,). for example, shen et al. () developed an integrative clustering approach (icluster) and used it to identify molecular subtypes for breast, lung and colon cancers. wang et al. () integrated different types of omic data using a hierarchical bayesian model called ‘integrative […]

PMCID: 5824897
PMID: 29497285
DOI: 10.1177/1177932218759292

[…] number of features or when the real associations between molecular features are known to be much smaller than all the possible associations., shen et al proposed a penalty-based clustering method (icluster) to identify the number of clusters and membership of clusters for the integrated genetic and genomic features (copy number variation [cnv], dna methylation, snp). the main idea is to treat […]

PMCID: 5840539
PMID: 29437778
DOI: 10.15252/emmm.201708274

[…] integration of copy number and transcript data from radical prostatectomy specimens (ross‐adams et al, ). indeed, the expression of melk tends to be higher in groups associated with poor prognosis (icluster 1, icluster 3 and icluster 5) than those associated with good prognosis (icluster 2 and icluster 4; figs b and d; ross‐adams et al, ; dunning et al, ). a number of publications suggest […]

PMCID: 5788352
PMID: 29377909
DOI: 10.1371/journal.pone.0191701

[…] true value. oncoprinter and mutationmapper tools were used for visualization of mutational data [, ]. integrative cluster analysis of mutation and copy number data was performed using the r package iclusterplus []., mutual exclusion and co-occurrence test for mutations (including both single nucleotide variants and copy number alterations) found in the 14 genes evaluated, were based on weighted […]

PMCID: 5701248
PMID: 29176703
DOI: 10.1038/s41467-017-01877-7

[…] ain 2000 probes with the highest mad across samples. these β values were then logit-transformed into m-values., the resulting four matrices were used as input to integrative clustering analysis using iclusterplus. a plot relating the percentage of explained variation to the number of clusters suggested five clusters as an appropriate choice for clustering the 256 scchn samples (supplementary fig.  […]


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iCluster institution(s)
Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY; Department of Epidemiology and Biostatistics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA; Department of Pathology and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
iCluster funding source(s)
Supported by a Starr Cancer Consortium grant and a National Institutes of Health grant U24 CA143840.

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