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


No version available



  • person_outline Ivana Ihnatova

Publication for ToPASeq

ToPASeq citation


Uterine glands impact uterine receptivity, luminal fluid homeostasis and blastocyst implantation

Sci Rep
PMCID: 5131473
PMID: 27905495
DOI: 10.1038/srep38078
call_split See protocol

[…] as 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) whic […]

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

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