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

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MotifDb")
AuthorPaul Shannon
Bioconductor views MotifAnnotation
Date of publicationNone
MaintainerPaul Shannon <pshannon@systemsbiology.org>
LicenseArtistic-2.0 | file LICENSE
Version1.16.1

View on Bioconductor

Functions

class:MotifList Man page
export Man page
export,MotifList,character,character-method Man page
export,MotifList,connection,character-method Man page
export,MotifList-method Man page
export,MotifList,missing,character-method Man page
MotifDb Man page
MotifDb-package Man page
MotifList-class Man page
query Man page
query,MotifList-method Man page
show,MotifList-method Man page
subset,MotifList-method Man page

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.