TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

Author
Ge Tan [aut, cre]
Date of publication
None
Maintainer
Ge Tan <ge.tan09@imperial.ac.uk>
License
GPL-2
Version
1.12.1
URLs

View on Bioconductor

Man pages

calConservation-methods
calConservation method
deleteMatrixHavingID-methods
JASPAR database operations
dmmEM-methods
dmmEM method
getEmissionProb
Get the emission distribution parameters.
getMatrixByID-methods
Basic JASPAR database search functionis 'getMatrixByID',...
getMatrixSet-methods
Advanced JASPAR database search functions 'get_MatrixSet'
getPosProb
Get the emission probabilities of nucleotides
IUPAC2Matrix
IUPAC2Matrix
MA0004.1
Some example PFM matrices.
makeFlatFileDir
Generate "FlatFileDir" directory
MotifSet-class
Class '"MotifSet"'
permuteMatrix-methods
permuteMatrix method
PFMSimilarity-methods
PFMSimilarity method
PWMSimilarity-methods
PWMSimilarity method
readJASPARMatrix
Read JASPAR format matrix
readXMLTFFM
readXMLTFFM
rPWMDmm-methods
rPWMDmm method
runMEME-methods
Wrapper function for MEME
sampleRanges
sampleRanges
searchAln-methods
searchAln method
searchPairBSgenome-methods
searchPairBSgenome method
searchSeq-methods
searchSeq method
seqLogo
Plot a sequence logo
shannon.entropy
Calculate the Shannon entropy
SitePairSet-class
Class '"SitePairSet"'
SitePairSetList-class
Class '"SitePairSetList"'
SiteSet-class
Class '"SiteSet"'
SiteSetList-class
Class '"SiteSetList"'
TFBSTools-package
TFBS software package.
TFFM-class
The TFFM class
toGRangesList-methods
toGRangesList function
toICM-methods
toICM method
toPWM-methods
toPWM method
writeGFF3-methods
'writeGFF3', 'writeGFF2' functions
XMatrix-class
'"XMatrix"' objects
XMatrixList-class
Class '"XMatrixList"'

Files in this package

TFBSTools/DESCRIPTION
TFBSTools/NAMESPACE
TFBSTools/NEWS
TFBSTools/R
TFBSTools/R/AllClasses.r
TFBSTools/R/AllGenerics.r
TFBSTools/R/DB-methods.r
TFBSTools/R/DirichletMixture.r
TFBSTools/R/Enrichment.R
TFBSTools/R/ICM-methods.r
TFBSTools/R/IO.R
TFBSTools/R/JASPAR.R
TFBSTools/R/Motif-methods.r
TFBSTools/R/PFM-methods.r
TFBSTools/R/PWM-methods.r
TFBSTools/R/PairwiseAlignment-methods.r
TFBSTools/R/SiteSet-methods.r
TFBSTools/R/TFFM.R
TFBSTools/R/TFFMseqLogo.R
TFBSTools/R/Wrappers-methods.r
TFBSTools/R/XMatrix-methods.r
TFBSTools/R/XMatrixList-methods.r
TFBSTools/R/coercion-methods.r
TFBSTools/R/show-methods.r
TFBSTools/R/util-methods.r
TFBSTools/build
TFBSTools/build/vignette.rds
TFBSTools/data
TFBSTools/data/MA0003.2.rda
TFBSTools/data/MA0004.1.rda
TFBSTools/data/MA0043.rda
TFBSTools/data/MA0048.rda
TFBSTools/inst
TFBSTools/inst/CITATION
TFBSTools/inst/TFBSToolsBuild
TFBSTools/inst/TFBSToolsBuild/build.r
TFBSTools/inst/TFBSToolsBuild/build2.R
TFBSTools/inst/TFBSToolsBuild/timing.R
TFBSTools/inst/doc
TFBSTools/inst/doc/TFBSTools.R
TFBSTools/inst/doc/TFBSTools.Rmd
TFBSTools/inst/doc/TFBSTools.html
TFBSTools/inst/extdata
TFBSTools/inst/extdata/MA0001.1.pfm
TFBSTools/inst/extdata/crp0.s
TFBSTools/inst/extdata/hg19.danRer7.net.axt
TFBSTools/inst/extdata/pfm_all_example.txt
TFBSTools/inst/extdata/tffm_detailed.xml
TFBSTools/inst/extdata/tffm_first_order.xml
TFBSTools/inst/obsolete
TFBSTools/inst/obsolete/PairwiseAlignmentTFBS-class.Rd
TFBSTools/inst/obsolete/TFBSTools.Rnw
TFBSTools/inst/obsolete/matrixAligner.c
TFBSTools/man
TFBSTools/man/IUPAC2Matrix.Rd
TFBSTools/man/MA0004.1.Rd
TFBSTools/man/MotifSet-class.Rd
TFBSTools/man/PFMSimilarity-methods.Rd
TFBSTools/man/PWMSimilarity-methods.Rd
TFBSTools/man/SitePairSet-class.Rd
TFBSTools/man/SitePairSetList-class.Rd
TFBSTools/man/SiteSet-class.Rd
TFBSTools/man/SiteSetList-class.Rd
TFBSTools/man/TFBSTools-package.Rd
TFBSTools/man/TFFM-class.Rd
TFBSTools/man/XMatrix-class.Rd
TFBSTools/man/XMatrixList-class.Rd
TFBSTools/man/calConservation-methods.Rd
TFBSTools/man/deleteMatrixHavingID-methods.Rd
TFBSTools/man/dmmEM-methods.Rd
TFBSTools/man/getEmissionProb.Rd
TFBSTools/man/getMatrixByID-methods.Rd
TFBSTools/man/getMatrixSet-methods.Rd
TFBSTools/man/getPosProb.Rd
TFBSTools/man/makeFlatFileDir.Rd
TFBSTools/man/permuteMatrix-methods.Rd
TFBSTools/man/rPWMDmm-methods.Rd
TFBSTools/man/readJASPARMatrix.Rd
TFBSTools/man/readXMLTFFM.Rd
TFBSTools/man/runMEME-methods.Rd
TFBSTools/man/sampleRanges.Rd
TFBSTools/man/searchAln-methods.Rd
TFBSTools/man/searchPairBSgenome-methods.Rd
TFBSTools/man/searchSeq-methods.Rd
TFBSTools/man/seqLogo.Rd
TFBSTools/man/shannon.entropy.Rd
TFBSTools/man/toGRangesList-methods.Rd
TFBSTools/man/toICM-methods.Rd
TFBSTools/man/toPWM-methods.Rd
TFBSTools/man/writeGFF3-methods.Rd
TFBSTools/src
TFBSTools/src/Makevars
TFBSTools/src/Makevars.common
TFBSTools/src/Makevars.win
TFBSTools/src/R_init_TFBSTools.c
TFBSTools/src/TFBSTools.h
TFBSTools/src/matrixAlignerDynamic.c
TFBSTools/tests
TFBSTools/tests/testthat
TFBSTools/tests/testthat.R
TFBSTools/tests/testthat/test_PFM.R
TFBSTools/tests/testthat/test_TFFM.R
TFBSTools/tests/testthat/test_XMatrix-class.R
TFBSTools/tests/testthat/test_searchSeq.R
TFBSTools/vignettes
TFBSTools/vignettes/TFBSTools.Rmd
TFBSTools/vignettes/TFBSTools.bib