Changes in version 1.3.2 - Exporting function estimateTransitionProb to estimate transition probabilities from a sequence of states of a Markov chain Changes in version 1.2.1 - Bug fix of output paths to handle paths with '.' Changes in version 1.2.0 - Second release of epigraHMM on Bioconductor. Changes in version 1.0.8 - Minor bug fix in maxStepProb documentations Changes in version 1.0.7 - Exporting maxStepProb, which compute the MLE of initial and transition probabilities of a K-state HMM, as well as simulateMarkovChain, which simulates a Markov chain of length 'n' given a matrix of transition probabilities Changes in version 1.0.6 - Minor bug fix in controlEM documentation Changes in version 1.0.5 - Minor bug fix in callPatterns and info function (explict import of S4Vectors::mcols and utils::tail). - Exporting expStep function, which implements the E-step of EM algorithm (forward-backward & Viterbi algorithm) for a K-state HMM. Changes in version 1.0.4 - Adding function callPatterns to exp[ort] combinatorial patterns (or posterior probabilities) associated with a given set of genomic regions. - Adding function info to print summary statistics from epigraHMM output. This function will print the model's BIC, log-likelihood, and combinatorial patterns associated with mixture model components. - Adding new example dataset helas3 with ENCODE ChIP-seq data from broad epigenomic marks H3K27me3, H3K36me3, and EZH2. - Adding option to prune combinatorial patterns associated with rare states. See vignette for details. - In differential peak calling, epigraHMM now exports combinatorial pattern table. See vignette for details. - Improvement of the vignette to clarify epigraHMM's use of blacklisted regions and gap tracks. Changes in version 1.0.3 - Minor updates in the NEWS file as well as the README page. Changes in version 1.0.2 - epigraHMM now exports a function called segmentGenome that segments a given genome (e.g. 'mm10') into non-overlapping genomic windows while considering gap tracks and blacklisted regions. Changes in version 1.0.1 - Minor fix in the package DESCRIPTION file and version numbers Changes in version 1.0.0 - First release of epigraHMM on Bioconductor. - It is now possible to add normalizing offsets via addOffsets. - epigraHMM now uses hdf5 files to store all intermediate data during computation of the EM algorithm. Intermediate data include window-based HMM and mixture model posterior probabilities, and forward-backward probabilities. This change leads to a better memory utilization of the package.