Changes in version 1.25.1 + Bugfixes: - fixed issue with R4.3 ("cannot xtfrm data frames") - fixed documentation - updated description file Changes in version 1.21.2 - increased upper bound for enrichment model, allowing for a steeper increase in enrichment with CpG density. (Github PR \#9) Changes in version 1.21.1 + Bugfixes: - makeTable with one window (github PR \#8) Changes in version 1.7.4 + Reformated NEWS file Changes in version 1.7.3 + Adapted vignette to BiocManager installation process Changes in version 1.7.2 + Bugfixes: - addCoverage fixed fragment size sd for chromosomes with 1 read - addCoverage fixed missing regions in count_matrix for chromosomes without any reads Changes in version 1.7.1 + Bugfix: addCoverage crashes when there are no reads for chromosome/contig Changes in version 1.5.1 + Bugfix: Crash due to changes in getOverlaps Changes in version 1.3.2 + New feature: - select active BSgenome masks for pattern density estimation + Bugfix: - adaptions to changed behavior of GenomicRanges Changes in version 1.3.1 + transition to Github Changes in version 1.1.6 + New Feature: - addNewSample function Changes in version 1.1.5 + New Feature: - multicore support for GLM fitting Changes in version 1.1.4 + Bugfixes: - fitting of GLM crashed when applied genome wide on > 150 samples Changes in version 1.1.3 + Updated citation. + Runtime improvement: - direct implementation of quantile function using quantile function of gamma distribution Changes in version 1.1.2 + Bugfixes: - addCNV: Fixed crash when only one normal sample is present - addCoverage: fixed chr sorting issue in absence of bam index Changes in version 1.0.0 + first stable release Changes in version 0.99.6 + Bugfixes: - addCNV: check for sample table now checks specified files for CNV Changes in version 0.99.5 + New features - user level functions now have sample id check - more detailed tutorial, including case study + Bugfixes: - makeTable: fixed groupMeans without individual samples Changes in version 0.99.4 + New functions: - multicore support for bam file processing - memory and runtime optimizations + Bugfixes: - bug in consideration of zygosity of chromosomes Changes in version 0.99.3 + Bugfixes: - updated imported NAMESPACE Changes in version 0.99.2 + New functions: - option to set ploidity for chromosomes, i.e. to account for sex chromosomes + Bugfixes: - fixed bug resulting in NA values at quantile calculation for beta estimates - minor fixes + Documentation: - changed vignette builder to knitr/BiocStyle/html Changes in version 0.99.1 + Bugfixes: - fixed crashing plotCoverage with one sample - qseaPCA-show - typo in error-message of getOffset (rpw) - resolved namespace issues Changes in version 0.99.0 + Submission to Bioconductor