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
