HOPACH statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HOPACH

Tool usage distribution map

This map represents all the scientific publications referring to HOPACH per scientific context
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HOPACH specifications


Unique identifier OMICS_23804
Alternative name Hierarchical Ordered Partitioning And Collapsing Hybrid
Software type Application/Script
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 2.40.0
Stability Stable
methods, stats, graphics, BiocGenerics, Biobase, utils, grDevices, R(>=2.11.0), cluster
Maintained Yes




No version available



  • person_outline Mark van der Laan
  • person_outline Katherine Pollard

Publication for Hierarchical Ordered Partitioning And Collapsing Hybrid

HOPACH citations


Gene set analysis of post lactational mammary gland involution gene signatures in inflammatory and triple negative breast cancer

PLoS One
PMCID: 5884491
PMID: 29617367
DOI: 10.1371/journal.pone.0192689

[…] tional mammary gland have been conducted by Clarkson et al. [, ] and Stein et al. []. Clarkson et al. [] used the K means clustering method and Stein et al. used the self-organizing map in [] and the hierarchical ordered partitioning and collapsing hybrid (HOPACH) method in [] to find the patterns among differentially expressed genes in the post-lactational involution period. They discovered that […]


Predictors of breast cancer cell types and their prognostic power in breast cancer patients

BMC Genomics
PMCID: 5809864
PMID: 29433432
DOI: 10.1186/s12864-018-4527-y

[…] The clustering was done using the R HOPACH package [] setting cosine dissimilarity as the distance metric. Gene ontology was performed using DAVID (32) by setting the human genome as the background. […]


Recellularization of rat liver: An in vitro model for assessing human drug metabolism and liver biology

PLoS One
PMCID: 5788381
PMID: 29377912
DOI: 10.1371/journal.pone.0191892

[…] vel between any 2 time points. Genes that showed no statistical difference between any 2 time points (ANOVA P value >0.05) were removed. A robust Z-score was computed for each gene across the groups. HOPACH clustering was applied to the robust Z-scores to obtain gene clusters by using cosine-similarity as the distance metric between the genes for days 2, 15, and 28 []. Gene ontology analysis was p […]


Unique intrahepatic transcriptomics profiles discriminate the clinical phases of a chronic HBV infection

PLoS One
PMCID: 5491066
PMID: 28662087
DOI: 10.1371/journal.pone.0179920

[…] Unsupervised hierarchical ordered partitioning and collapsing hybrid (HOPACH) clustering was used on the top 50 modules to identify intrinsic functional clusters (IFC) which show dynamic modulation during the cour […]


Age dependent electrical and morphological remodeling of the Drosophila heart caused by hERG/seizure mutations

PLoS Genet
PMCID: 5459509
PMID: 28542428
DOI: 10.1371/journal.pgen.1006786

[…] lated genes where considered those with an absolute fold change greater than 2 and a P<0.05 in compared to each mutants control line (1812 probesets). Clustering was conducted in AltAnalyze using the HOPACH algorithm with cosign similarity. For Gene Ontology (GO) enrichment analysis, GO-Elite [] was used to find the enrichment of GO terms amongst the significantly up and downregulated genes (|Fold […]


Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome

PMCID: 5372339
PMID: 28356166
DOI: 10.1186/s13058-017-0812-y

[…] l measurement [, ]. The normalized mRNA expression and the 25% most variable copy number data were used for calculating inferred pathway levels (IPL) at five3genomics.com. Clustering was performed by HOPACH 2.10 [] in R version 3.0.0 [] and visualized using cluster 3.0 [] and Java TreeView ver.1.1.6r3 []. For the HOPACH hierarchical clustering algorithm, we used correlation distance “cor” and clus […]

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HOPACH institution(s)
Division of Biostatistics, School of Public Health Division of Biostatistics, University of California, Berkeley, CA, USA
HOPACH funding source(s)
Supported by a grant from the Life Sciences Informatics Program with industrial partner biotech company Chiron Corporation.

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