TROM: Transcriptome Overlap Measure

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.

Author
Jingyi Jessica Li <jli@stat.ucla.edu>, Wei Vivian Li <liw@ucla.edu>
Date of publication
2016-10-07 09:37:57
Maintainer
Jingyi Jessica Li <jli@stat.ucla.edu>
License
GPL-2
Version
1.2
URLs

View on CRAN

Man pages

bs.trom
Between-species transcriptome mapping
choose.z
Choose the suggested threshold of Z-scores
find.top.GO.slim.terms
Find top enriched GO slim terms
find.top.GO.terms
Find top enriched GO terms
GO_slim_id
GO slim IDs
heatmap.3
Plot TROM scores in a heatmap.
select.associated.genes
Select the associated genes for biological samples of a...
select.associated.orthologs
Select the associated genes for biological samples of a...
TROM-package
Transcriptome Overlap Measure
ws.trom
Within-species transcriptome mapping
ws.trom.orthologs
Within-species transcriptome mapping using ortholog genes

Files in this package

TROM
TROM/inst
TROM/inst/dm_ce_genelists.xlsx
TROM/inst/convert.py
TROM/inst/dm_associated_orthologs.xlsx
TROM/inst/dm_associated_genes.xlsx
TROM/inst/doc
TROM/inst/doc/TROM_Vignette.pdf
TROM/inst/doc/TROM-manual.pdf
TROM/NAMESPACE
TROM/data
TROM/data/GO_slim_id.rda
TROM/R
TROM/R/P_mass.R
TROM/R/sp.ortholog.z.R
TROM/R/find.top.GO.terms.R
TROM/R/choose.z.R
TROM/R/ws.trom.R
TROM/R/find.top.GO.slim.terms.R
TROM/R/select.associated.orthologs.R
TROM/R/count_GO_terms.R
TROM/R/bs.trom.R
TROM/R/select.associated.genes.R
TROM/R/ws.trom.orthologs.R
TROM/R/ws.trom.two.R
TROM/R/ws.trom.forZ.R
TROM/R/sp.associated.idx.R
TROM/R/enrichment_test.R
TROM/R/TROM-internal.R
TROM/R/heatmap.3.R
TROM/R/sp.std.R
TROM/R/find_top_GO_terms.R
TROM/R/write_top_GO_terms.R
TROM/R/ws.trom.three.R
TROM/R/heatmap.3.ddg.R
TROM/R/heatmap.3.noddg.R
TROM/MD5
TROM/DESCRIPTION
TROM/man
TROM/man/select.associated.orthologs.Rd
TROM/man/find.top.GO.slim.terms.Rd
TROM/man/heatmap.3.Rd
TROM/man/ws.trom.orthologs.Rd
TROM/man/find.top.GO.terms.Rd
TROM/man/select.associated.genes.Rd
TROM/man/TROM-package.Rd
TROM/man/bs.trom.Rd
TROM/man/choose.z.Rd
TROM/man/ws.trom.Rd
TROM/man/GO_slim_id.Rd