MotifDb: An Annotated Collection of Protein-DNA Binding Sequence Motifs
Version 1.18.0

More than 2000 annotated position frequency matrices from nine public sources, for multiple organisms.

Browse man pages Browse package API and functions Browse package files

AuthorPaul Shannon
Bioconductor views MotifAnnotation
Date of publicationNone
MaintainerPaul Shannon <pshannon@systemsbiology.org>
LicenseArtistic-2.0 | file LICENSE
Version1.18.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MotifDb")

Man pages

export: export
MotifDb: MotifDb: An Annotated Collection of DNA-binding sequence...
MotifList-class: MotifList
query: query
subset: subset

Functions

MotifDb Man page Source code
MotifDb-package Man page
MotifList Source code
MotifList-class Man page
class:MotifList Man page
export Man page
export,MotifList,character,character-method Man page
export,MotifList,connection,character-method Man page
export,MotifList,missing,character-method Man page
export,MotifList-method Man page
matrixToMemeText Source code
onLoad Source code
query Man page
query,MotifList-method Man page Man page
show,MotifList-method Man page Man page
subset,MotifList-method Man page Man page
transformMatrixToMemeRepresentation Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/MotifList-class.R
R/zzz.R
build
build/vignette.rds
inst
inst/doc
inst/doc/MotifDb.R
inst/doc/MotifDb.Rnw
inst/doc/MotifDb.pdf
inst/extdata
inst/extdata/ScerTF.RData
inst/extdata/cisbp.RData
inst/extdata/flyFactorSurvey.RData
inst/extdata/hPDI.RData
inst/extdata/jaspar.RData
inst/extdata/jaspar2014.RData
inst/extdata/jolma2013.RData
inst/extdata/stamlab.RData
inst/extdata/uniprobe.RData
inst/makefile
inst/scripts
inst/scripts/import
inst/scripts/import/HOCOMOCO
inst/scripts/import/HOCOMOCO/import.R
inst/scripts/import/HOCOMOCO/import_functional_only_matrices.R
inst/scripts/import/HOCOMOCO/test.R
inst/scripts/import/HOCOMOCO/test.txt
inst/scripts/import/README
inst/scripts/import/ScerTF
inst/scripts/import/ScerTF/import.R
inst/scripts/import/ScerTF/test.R
inst/scripts/import/cisbp
inst/scripts/import/cisbp/cisbp-metadata-6559-matrices.Rdata
inst/scripts/import/cisbp/import.R
inst/scripts/import/cisbp/test.R
inst/scripts/import/demo
inst/scripts/import/demo/import.R
inst/scripts/import/demo/md-raw.tsv
inst/scripts/import/demo/sample.pcm
inst/scripts/import/fbgns.RData
inst/scripts/import/flyFactorSurvey
inst/scripts/import/flyFactorSurvey/import.R
inst/scripts/import/flyFactorSurvey/test.R
inst/scripts/import/hPDI
inst/scripts/import/hPDI/import.R
inst/scripts/import/hPDI/test.R
inst/scripts/import/importAll.R
inst/scripts/import/jaspar
inst/scripts/import/jaspar/import.R
inst/scripts/import/jaspar/test.R
inst/scripts/import/jaspar2014
inst/scripts/import/jaspar2014/import.R
inst/scripts/import/jaspar2014/jaspar2014
inst/scripts/import/jaspar2014/jaspar2014/MATRIX_ANNOTATION.txt
inst/scripts/import/jaspar2014/jaspar2014/MATRIX_PROTEIN.txt
inst/scripts/import/jaspar2014/jaspar2014/MATRIX_SPECIES.txt
inst/scripts/import/jaspar2014/jaspar2014/Matrix.txt
inst/scripts/import/jaspar2014/jaspar2014/matrix_data.txt
inst/scripts/import/jaspar2014/md-raw.tsv
inst/scripts/import/jaspar2014/sample.pcm
inst/scripts/import/jaspar2014/test.R
inst/scripts/import/jolma2013
inst/scripts/import/jolma2013/import.R
inst/scripts/import/jolma2013/test.R
inst/scripts/import/stamlab
inst/scripts/import/stamlab/import.R
inst/scripts/import/stamlab/test.R
inst/scripts/import/uniprobe
inst/scripts/import/uniprobe/import.R
inst/scripts/import/uniprobe/test.R
inst/unitTests
inst/unitTests/test_MotifDb.R
inst/vanillaTest.R
man
man/MotifDb.Rd
man/MotifList-class.Rd
man/export.Rd
man/query.Rd
man/subset.Rd
notInstalled
notInstalled/hidden
notInstalled/hidden/MotifDb-package.Rd
notInstalled/hidden/MotifList.Rd-hidden
notInstalled/hidden/ScerTF.Rd
notInstalled/hidden/flyFactorSurvey.Rd
notInstalled/hidden/hPDI.Rd
notInstalled/hidden/jaspar.Rd
notInstalled/hidden/matrices.Rd
notInstalled/hidden/tbl.md.Rd
notInstalled/hidden/uniprobe.Rd
test.txt
tests
tests/runTests.R
vignettes
vignettes/MotifDb.Rnw
vignettes/programmersGuide.txt
MotifDb documentation built on May 20, 2017, 10:21 p.m.