HOPACH statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HOPACH
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Tool usage distribution map

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

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Protocols

HOPACH specifications

Information


Unique identifier OMICS_23804
Name HOPACH
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
Requirements
methods, stats, graphics, BiocGenerics, Biobase, utils, grDevices, R(>=2.11.0), cluster
Maintained Yes

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Documentation


Maintainers


  • person_outline Mark van der Laan
  • person_outline Katherine Pollard

Publication for Hierarchical Ordered Partitioning And Collapsing Hybrid

HOPACH citations

 (47)
library_books

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

2018
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 […]

library_books

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

2018
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. […]

library_books

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

2018
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 […]

library_books

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

2017
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 […]

library_books

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

2017
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 […]

library_books

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

2017
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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