Files in ge11232002/TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) Analysis
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/AllClasses.r
R/AllGenerics.r
R/DB-methods.r
R/DirichletMixture.r
R/Enrichment.R
R/ICM-methods.r
R/IO.R
R/JASPAR.R
R/Motif-methods.r
R/PFM-methods.r
R/PWM-methods.r
R/PairwiseAlignment-methods.r
R/SiteSet-methods.r
R/TFFM.R
R/TFFMseqLogo.R
R/Wrappers-methods.r
R/XMatrix-methods.r
R/XMatrixList-methods.r
R/coercion-methods.r
R/show-methods.r
R/util-methods.r
README.md
TFBSTools.Rproj
data/MA0003.2.rda
data/MA0004.1.rda
data/MA0043.rda
data/MA0048.rda
inst/CITATION
inst/TFBSToolsBuild/build.r
inst/TFBSToolsBuild/build2.R
inst/TFBSToolsBuild/timing.R
inst/extdata/MA0001.1.pfm
inst/extdata/crp0.s
inst/extdata/hg19.danRer7.net.axt
inst/extdata/meme.output
inst/extdata/pfm_all_example.txt
inst/extdata/tffm_detailed.xml
inst/extdata/tffm_first_order.xml
inst/obsolete/PairwiseAlignmentTFBS-class.Rd
inst/obsolete/TFBSTools.Rnw
inst/obsolete/matrixAligner.c
man/IUPAC2Matrix.Rd
man/MA0004.1.Rd
man/MotifSet-class.Rd
man/PFMSimilarity-methods.Rd
man/PWMSimilarity-methods.Rd
man/SitePairSet-class.Rd
man/SitePairSetList-class.Rd
man/SiteSet-class.Rd
man/SiteSetList-class.Rd
man/TFBSTools-package.Rd
man/TFFM-class.Rd
man/XMatrix-class.Rd
man/XMatrixList-class.Rd
man/calConservation-methods.Rd
man/deleteMatrixHavingID-methods.Rd
man/dmmEM-methods.Rd
man/getEmissionProb.Rd
man/getMatrixByID-methods.Rd
man/getMatrixSet-methods.Rd
man/getPosProb.Rd
man/makeFlatFileDir.Rd
man/parseMEMEOutput.Rd
man/permuteMatrix-methods.Rd
man/rPWMDmm-methods.Rd
man/readJASPARMatrix.Rd
man/readXMLTFFM.Rd
man/runMEME-methods.Rd
man/sampleRanges.Rd
man/searchAln-methods.Rd
man/searchPairBSgenome-methods.Rd
man/searchSeq-methods.Rd
man/seqLogo.Rd
man/shannon.entropy.Rd
man/toGRangesList-methods.Rd
man/toICM-methods.Rd
man/toPWM-methods.Rd
man/writeGFF3-methods.Rd
src/Makevars
src/Makevars.common
src/Makevars.win
src/R_init_TFBSTools.c
src/TFBSTools.h
src/matrixAlignerDynamic.c
tests/testthat.R
tests/testthat/test_Coercion.R
tests/testthat/test_MEME.R
tests/testthat/test_PFM.R
tests/testthat/test_TFFM.R
tests/testthat/test_XMatrix-class.R
tests/testthat/test_searchSeq.R
vignettes/.gitignore
vignettes/TFBSTools.Rmd
vignettes/TFBSTools.bib
