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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
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Documentation
Maintainer
- person_outline Ivana Ihnatova <>
Publication for ToPASeq
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data.
ToPASeq in publications
(3)[…] 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 […]
Acute effects of focused ultrasound induced increases in blood brain barrier permeability on rat microvascular transcriptome
[…] 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 […]
Uterine glands impact uterine receptivity, luminal fluid homeostasis and blastocyst implantation
[…] 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) […]
ToPASeq reviews
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