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. 14, 2023, 5:13 a.m.