Files in motifcounter

R package for analysing TFBSs in DNA sequences

README.md

NEWS

NAMESPACE

DESCRIPTION

.zenodo.json

build/vignette.rds

src/score2d.h

src/simulate.h

src/mdist_register.c

src/simulate.c

src/background.c

src/score1d.c

src/sequence.c

src/scorefunctions.h

src/combinatorial.h

src/scorefunctions.c

src/combinatorial.c

src/Rminmaxscore.c

src/Rcombinatorial.c

src/sequence.h

src/matrix.h

src/minmaxscore.h

src/markovchain.h

src/Makevars

src/overlap.c

src/matrix.c

src/markovchain_single.c

src/Rbackground.c

src/score1d.h

src/background.h

src/compoundpoisson.h

src/markovchain.c

src/Roption.h

src/Roption.c

src/minmaxscore.c

src/overlap.h

src/Rsimulate.c

src/Roverlap.c

src/score2d.c

src/compoundpoisson.c

src/Rsequence.c

src/Rscore1d.c

src/Rcompoundpoisson.c

R/score_wrapper.R R/observed_wrapper.R R/background_wrapper.R R/combinatorial_wrapper.R R/option.R R/comppoiss_wrapper.R R/overlap.R R/forground_wrapper.R R/simulate_wrapper.R R/count_wrapper.R R/motifcounter-package.R R/markovmodel.R R/wrapper.R R/enrichmentTest.R man-roxygen/templates.R vignettes/motifcounter.Rmd

vignettes/literature.bib

vignettes/motifcounter.css

man/getAlpha.Rd man/markovModel.Rd man/generateDNAStringSet.Rd man/motifValid.Rd man/getGamma.Rd man/numMotifHits.Rd man/generateDNAString.Rd man/lenSequences.Rd man/scoreDistEmpirical.Rd man/getTrans.Rd man/scoreStrand.Rd man/motifHitProfile.Rd man/readBackground.Rd man/motifAndBackgroundValid.Rd man/combinatorialDist.Rd man/scoreSequence.Rd man/getBeta5p.Rd man/probOverlapHit.Rd man/getOrder.Rd man/sigLevel.Rd man/getBeta.Rd man/getCounts.Rd man/normalizeMotif.Rd man/motifEnrichment.Rd man/Overlap-class.Rd man/scoreDistBf.Rd man/computeClumpStartProb.Rd man/simulateClumpSizeDist.Rd man/clumpSizeDist.Rd man/scoreThreshold.Rd man/hitStrand.Rd man/simulateNumHitsDist.Rd man/revcompMotif.Rd man/motifHits.Rd man/getSinglestranded.Rd man/scoreDist.Rd man/scoreHistogram.Rd man/motifcounterOptions.Rd man/Background-class.Rd man/compoundPoissonDist.Rd man/scoreProfile.Rd man/motifcounter-package.Rd man/scoreHistogramSingleSeq.Rd man/getBeta3p.Rd man/getStation.Rd tests/testthat.R tests/testthat/testcombinatorial.R tests/testthat/testsimulate.R tests/testthat/testenrichment.R tests/testthat/testobserved.R tests/testthat/testoverlap.R tests/testthat/testcomppoiss.R tests/testthat/testoptions.R tests/testthat/testmotif.R tests/testthat/testbackground.R tests/testthat/testcount.R tests/testthat/testmarkov.R tests/testthat/testscore.R

inst/CITATION

inst/doc/motifcounter.Rmd

inst/doc/motifcounter.html

inst/doc/motifcounter.R

inst/extdata/seq.fasta

inst/extdata/seq2.fasta

inst/extdata/test.tab

inst/extdata/x21.tab

inst/extdata/m2.tab

inst/extdata/test.fa

inst/extdata/x8.tab

inst/extdata/oct4_chipseq.fa

inst/extdata/x1.tab

inst/extdata/m1.tab

inst/extdata/x3.tab

inst/extdata/seq1.fasta

inst/extdata/x31.tab

inst/extdata/test2.fa

inst/extdata/x32.tab

inst/extdata/m12.tab

motifcounter documentation built on Nov. 8, 2020, 5:44 p.m.