triform: Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data

The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("triform")
AuthorKarl Kornacker Developer [aut], Tony Handstad Developer [aut, cre]
Bioconductor views ChIPSeq Sequencing
Date of publicationNone
MaintainerThomas Carroll <tc.infomatics@gmail.com>
LicenseGPL-2
Version1.18.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/preprocess.R R/triform.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/GPL.txt
inst/doc/triform.R
inst/doc/triform.Rnw
inst/doc/triform.pdf
inst/extdata
inst/extdata/backgr_huds_Gm12878_rep1.bed
inst/extdata/backgr_huds_Gm12878_rep2.bed
inst/extdata/config.yml
inst/extdata/srf_huds_Gm12878_rep1.bed
inst/extdata/srf_huds_Gm12878_rep2.bed
inst/unitTests
inst/unitTests/data
inst/unitTests/data/t1
inst/unitTests/data/t1/mockdata.bed
inst/unitTests/data/t2
inst/unitTests/data/t2/mockdata.RData
inst/unitTests/data/t3
inst/unitTests/data/t3/chrX.RData
inst/unitTests/data/t3/chrX_mockdata.RData
inst/unitTests/data/t3/chrY.RData
inst/unitTests/data/t3/chrY_mockdata.RData
inst/unitTests/test_preprocess.R
man
man/preprocess.Rd man/triform-package.Rd man/triform.Rd
tests
tests/runTests.R triform-Ex.R
vignettes
vignettes/auto
vignettes/auto/triform.el
vignettes/triform.Rnw
vignettes/triform.bib

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