Tspair pipeline

Tspair specifications


Unique identifier OMICS_12484
Name Tspair
Alternative name Top Scoring Pairs
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Either (i) a gene expression matrix or an expression set and a group indicator vector, or (ii) an expression set object and a column number, indicating which column of the annotation data to use as the group indicator.
Output data A tsp object which gives the TSP score, indices, gene expression data and group labels for the TSP. If there are multiple pairs that achieve the top score, then the tie-breaking score developed by Tan et al. (2005) is reported.
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.30.0
Stability Stable
Requirements R, Biobase
Maintained Yes



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  • person_outline Jeffrey T. Leek <>

Publication for Top Scoring Pairs

Tspair IN pipeline

PMCID: 5807776
PMID: 29426285
DOI: 10.1186/s12864-018-4505-4

[…] level of 0.1., fragments per kilobase per million reads (fpkm) were calculated using the function “rpkm()” from “edger”. fpkm was the used as input for the calculation of tsp using the package “tspair” [66]. the tsp approach [45] identifies genes whose transcript abundance ratios within each individual can classify subjects into binary categories. the ratios of the 20 tsp were used as input […]

Tspair institution(s)
Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
Tspair funding source(s)
National Science Foundation (DMS034211); National Institutes of Health (1UL1RR025005-01).

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