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TROM (version 1.3)

Transcriptome Overlap Measure

Description

A new bioinformatic tool for comparing transcriptomes of two biological samples from the same or different species. The mapping is conducted based on the overlap of the associated genes of different samples. More examples and detailed explanations are available in the vignette. For detailed description of the method, please refer to Li, Wei Vivian, Yiling Chen, and Jingyi Jessica Li. "TROM: A testing-based method for finding transcriptomic similarity of biological samples." Statistics in biosciences 9.1 (2017): 105-136 .

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Version

Install

install.packages('TROM')

Monthly Downloads

18

Version

1.3

License

GPL-2

Maintainer

Jingyi Jessica Li

Last Published

July 2nd, 2018

Functions in TROM (1.3)

find.top.GO.terms

Find top enriched GO terms
bs.trom

Between-species transcriptome mapping
select.associated.genes

Select the associated genes for biological samples of a species
select.associated.orthologs

Select the associated genes for biological samples of a species among the genes with orthologs in the other species
ws.trom.orthologs

Within-species transcriptome mapping using ortholog genes
GO_slim_id

GO slim IDs
TROM-package

Transcriptome Overlap Measure
ws.trom

Within-species transcriptome mapping
find.top.GO.slim.terms

Find top enriched GO slim terms
choose.z

Choose the suggested threshold of Z-scores
heatmap.3

Plot TROM scores in a heatmap.