Files in plbaldoni/epigraHMM

Epigenomic R-based analysis with hidden Markov models

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/RcppExports.R R/addOffsets.R R/base-EM.R R/base-checkers.R R/base-core.R R/base-loglikelihood.R R/base-optim.R R/base-utils.R R/base-wrappers.R R/base-writers.R R/callPaterns.R R/callPeaks.R R/cleanCounts.R R/controlEM.R R/data-helas3.R R/epigraHMM-package.R R/epigraHMM.R R/epigraHMMDataSetFromBam.R R/epigraHMMDataSetFromMatrix.R R/estimateTransitionProb.R R/info.R R/initializer.R R/normalizeCounts.R R/plotCounts.R R/plotPatterns.R R/segmentGenome.R R/utils-data-table.R R/utils-pipe.R README.Rmd README.md

data/helas3.rda

man/addOffsets.Rd man/callPatterns.Rd man/callPeaks.Rd man/cleanCounts.Rd man/controlEM.Rd man/epigraHMM.Rd man/epigraHMMDataSetFromBam.Rd man/epigraHMMDataSetFromMatrix.Rd man/estimateTransitionProb.Rd man/expStep.Rd man/helas3.Rd man/info.Rd man/initializer.Rd man/maxStepProb.Rd man/normalizeCounts.Rd man/plotCounts.Rd man/plotPatterns.Rd man/segmentGenome.Rd man/simulateMarkovChain.Rd

src/.gitignore

src/Makevars

src/Makevars.win

src/RcppExports.cpp

src/aggregate.cpp

src/aggregate.h

src/computeBIC.cpp

src/computeQFunction.cpp

src/computeViterbiSequence.cpp

src/consensusRejectionControlled.cpp

src/differentialRejectionControlled.cpp

src/expStep.cpp

src/getMarginalProbability.cpp

src/innerMaxStepProb.cpp

src/maxStepProb.cpp

src/rbinomVectorized.cpp

src/rbinomVectorized.h

src/reweight.cpp

src/reweight.h

src/simulateMarkovChain.cpp

tests/testthat.R tests/testthat/test-addOffsets.R tests/testthat/test-base.R tests/testthat/test-callPeaks.R tests/testthat/test-cleanCounts.R tests/testthat/test-controlEM.R tests/testthat/test-epigraHMM.R tests/testthat/test-epigraHMMDataSetFromBam.R tests/testthat/test-epigraHMMDataSetFromMatrix.R tests/testthat/test-initializer.R tests/testthat/test-normalizeCounts.R tests/testthat/test-plotCounts.R tests/testthat/test-plotPatterns.R

vignettes/.gitignore

vignettes/bibliography.bib

vignettes/epigraHMM.Rmd

plbaldoni/epigraHMM documentation built on Oct. 15, 2023, 7:53 p.m.