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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



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  • person_outline Mark van der Laan <>
  • person_outline Katherine Pollard <>

Publication for Hierarchical Ordered Partitioning And Collapsing Hybrid

HOPACH in publications

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

[…] 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 […]

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

[…] on the original 308 predictors for further analysis., next, we investigated the expression patterns of the 308 predictors (34 lncrnas + 274 pcgs) across the 6 different cell types by performing hopach clustering using cosine dissimilarity as the distance metric. this yielded 8 optimal clusters (fig. ). interestingly 6 clusters showed a restricted expression pattern to one single cell type […]

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

[…] the ic, and the eneg phase for individual modules were used to rank all 260 modules. the modules ranked within the upper 10 percentile were selected as the top varied modules (n = 50)., 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 […]

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

[…] 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 […]

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

[…] 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” […]

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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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