TROM: Transcriptome Overlap Measure
Version 1.2

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.

Browse man pages Browse package API and functions Browse package files

AuthorJingyi Jessica Li <jli@stat.ucla.edu>, Wei Vivian Li <liw@ucla.edu>
Date of publication2016-10-07 09:37:57
MaintainerJingyi Jessica Li <jli@stat.ucla.edu>
LicenseGPL-2
Version1.2
URL http://www.stat.ucla.edu/~jingyi.li/software-and-data/trom.html http://www.stat.ucla.edu/~jingyi.li/packages/TROM/vignette.pdf
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("TROM")

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

Functions

GO_slim_id Man page
P_mass Source code
TROM Man page
TROM-package Man page
bs.trom Man page Source code
choose.z Man page Source code
count_GO_terms Source code
enrichment_test Source code
find.top.GO.slim.terms Man page Source code
find.top.GO.terms Man page Source code
find_top_GO_terms Source code
heatmap.3 Man page Source code
heatmap.3.ddg Source code
heatmap.3.noddg Source code
select.associated.genes Man page Source code
select.associated.orthologs Man page Source code
sp.associated.idx Source code
sp.ortholog.z Source code
sp.std Source code
write_top_GO_terms Source code
ws.trom Man page Source code
ws.trom.forZ Source code
ws.trom.orthologs Man page Source code
ws.trom.three Source code
ws.trom.two Source code

Files

inst
inst/dm_ce_genelists.xlsx
inst/convert.py
inst/dm_associated_orthologs.xlsx
inst/dm_associated_genes.xlsx
inst/doc
inst/doc/TROM_Vignette.pdf
inst/doc/TROM-manual.pdf
NAMESPACE
data
data/GO_slim_id.rda
R
R/P_mass.R
R/sp.ortholog.z.R
R/find.top.GO.terms.R
R/choose.z.R
R/ws.trom.R
R/find.top.GO.slim.terms.R
R/select.associated.orthologs.R
R/count_GO_terms.R
R/bs.trom.R
R/select.associated.genes.R
R/ws.trom.orthologs.R
R/ws.trom.two.R
R/ws.trom.forZ.R
R/sp.associated.idx.R
R/enrichment_test.R
R/TROM-internal.R
R/heatmap.3.R
R/sp.std.R
R/find_top_GO_terms.R
R/write_top_GO_terms.R
R/ws.trom.three.R
R/heatmap.3.ddg.R
R/heatmap.3.noddg.R
MD5
DESCRIPTION
man
man/select.associated.orthologs.Rd
man/find.top.GO.slim.terms.Rd
man/heatmap.3.Rd
man/ws.trom.orthologs.Rd
man/find.top.GO.terms.Rd
man/select.associated.genes.Rd
man/TROM-package.Rd
man/bs.trom.Rd
man/choose.z.Rd
man/ws.trom.Rd
man/GO_slim_id.Rd
TROM documentation built on May 19, 2017, 9:27 p.m.