ToPASeq specifications
Information
| 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 |
| Requirements |
methods, BiocStyle, Rcpp, rmarkdown, knitr, graph, airway, R(>=3.5.0), graphite, EnrichmentBrowser
|
| Maintained | Yes |
Versioning
No version available
Documentation
Maintainer
- person_outline Ivana Ihnatova
Publication for ToPASeq
library_books
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
2015 BMC Bioinformatics
PMCID: 4625615
PMID: 26514335
DOI: 10.1186/s12859-015-0763-1
ToPASeq citation
call_split
Uterine glands impact uterine receptivity, luminal fluid homeostasis and blastocyst implantation
[…] 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
ToPASeq reviews
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