# epigraHMM 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. # epigraHMM 1.0.1 * Minor fix in the package DESCRIPTION file and version numbers # epigraHMM 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. # epigraHMM 1.0.3 * Minor updates in the NEWS file as well as the README page. # epigraHMM 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. # epigraHMM 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. # epigraHMM 1.0.6 * Minor bug fix in controlEM documentation # epigraHMM 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 # epigraHMM 1.0.8 * Minor bug fix in maxStepProb documentations # epigraHMM 1.2.0 * Second release of epigraHMM on Bioconductor. # epigraHMM 1.2.1 * Bug fix of output paths to handle paths with '.' # epigraHMM 1.3.2 * Exporting function estimateTransitionProb to estimate transition probabilities from a sequence of states of a Markov chain # epigraHMM 1.7.1/1.6.3 * Fix callPeaks function to export .bed, .wig, and .bedGraph files * Output files are now overwritten, if existing # epigraHMM 1.7.2/1.6.4 * Fix callPeaks writers so that it works on Windows # epigraHMM 1.9.1/1.8.2 * Fix normalization of log-probabilities in cpp code to avoid underflow