NEWS

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qsea 1.25.1

• Bugfixes: - fixed issue with R4.3 ("cannot xtfrm data frames") - fixed documentation - updated description file

qsea 1.21.2

• increased upper bound for enrichment model, allowing for a steeper increase in enrichment with CpG density. (Github PR \#9)

qsea 1.21.1

• Bugfixes: - makeTable with one window (github PR \#8)

qsea 1.7.4

• Reformated NEWS file

qsea 1.7.3

• Adapted vignette to BiocManager installation process

qsea 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

qsea 1.7.1

• Bugfix: addCoverage crashes when there are no reads for chromosome/contig

qsea 1.5.1

• Bugfix: Crash due to changes in getOverlaps

qsea 1.3.2

• New feature: - select active BSgenome masks for pattern density estimation
• Bugfix: - adaptions to changed behavior of GenomicRanges

qsea 1.3.1

• transition to Github

qsea 1.1.6

• New Feature: - addNewSample function

qsea 1.1.5

• New Feature: - multicore support for GLM fitting

qsea 1.1.4

• Bugfixes: - fitting of GLM crashed when applied genome wide on > 150 samples

qsea 1.1.3

• Updated citation.
• Runtime improvement: - direct implementation of quantile function using quantile function of gamma distribution

qsea 1.1.2

• Bugfixes: - addCNV: Fixed crash when only one normal sample is present - addCoverage: fixed chr sorting issue in absence of bam index

qsea 1.0.0

• first stable release

qsea 0.99.6

• Bugfixes: - addCNV: check for sample table now checks specified files for CNV

qsea 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

qsea 0.99.4

• New functions: - multicore support for bam file processing - memory and runtime optimizations
• Bugfixes: - bug in consideration of zygosity of chromosomes

qsea 0.99.3

• Bugfixes: - updated imported NAMESPACE

qsea 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

qsea 0.99.1

• Bugfixes: - fixed crashing plotCoverage with one sample - qseaPCA-show - typo in error-message of getOffset (rpw) - resolved namespace issues

qsea 0.99.0

• Submission to Bioconductor