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.

AuthorGe Tan [aut, cre]
Date of publicationNone
MaintainerGe Tan <ge.tan09@imperial.ac.uk>
LicenseGPL-2
Version1.12.1
https://github.com/ge11232002/TFBSTools

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

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