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ToPASeq specifications


Unique identifier OMICS_10391
Name ToPASeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Affero General Public License version 3
Computer skills Advanced
Version 1.14.1
Stability Stable
methods, BiocStyle, Rcpp, rmarkdown, knitr, graph, airway, R(>=3.5.0), graphite, EnrichmentBrowser
Maintained Yes


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  • person_outline Ivana Ihnatova <>

Publication for ToPASeq

ToPASeq in publications

PMCID: 5784953
PMID: 29370226
DOI: 10.1371/journal.pone.0191154

[…] implementations of the selected topology-based pathway analysis methods: (i) original implementation (all but tappa), (ii) graphite package (spia, topologygsa, clipper, degraph) [] and (iii) topaseq package [] (all methods). topaseq package is our previous work in which we either de novo implemented or optimised existing implementations of a number of existing topology-based pathway […]

PMCID: 5379491
PMID: 28374753
DOI: 10.1038/srep45657

[…] groups if the log2 fold-change was greater or less than 1.0 or −1.0, respectively, and had an adjusted p-value of less than 0.05. a total of 19105 genes were assessed for differential expression., topaseq (bioconductor) was used to identify gene ontology (go) terms that were altered in microvessels by fus treatment. for both over-representation analysis (ora) and geneset enrichment analysis […]

PMCID: 5131473
PMID: 27905495
DOI: 10.1038/srep38078

[…] compared to wt mice were further analyzed to predict gene functions, pathways and networks. pathway analysis was performed by topology-based prediction method implemented in r-bioconductor package topaseq. over-representation of gene-ontology (go terms) were analyzed using bingo tool. biclusters analysis of gene expression was performed using the order-preserving submatrix algorithm (opsm) […]

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ToPASeq institution(s)
Institute of Biostatistics and Analyses, Faculty of Medicine, Masarykova Univerzita, Brno, Czech Republic

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