# 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