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

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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.

Author
Karl Kornacker Developer [aut], Tony Handstad Developer [aut, cre]
Date of publication
None
Maintainer
Thomas Carroll <tc.infomatics@gmail.com>
License
GPL-2
Version
1.16.0

View on Bioconductor

Man pages

preprocess
Preprocess BED-files with reads to calculate chromosome...
triform
Run Triform peak detection algorithm.
triform-package
Triform finds peaks in ChIP-sequencing data.

Files in this package

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