Changes in version 2.5.2
+ Added `summariseOverrep()`

Changes in version 2.5.1
+ Changed method for setting default theme using plotTheme
+ Set factor levels for plotSeqContent for FastpDataList
+ Added line & cumulative plotTypes for plotInsertSize

Changes in version 2.3.5
+ added support for rnaseqc metrics files

Changes in version 2.1.5
+ Added FastpData and FastpDataList classes for working with fastp reports

Changes in version 2.1.4
+ Added umi_tools dedup to importNgsLogs

Changes in version 2.1.3
+ Bugfix when importing duplicationMetrics

Changes in version 2.0.0
+ Added status bar to all plots from FastQC reports using pachwork

Changes in version 1.13.3
+ Bug fix for importing macs2 logs

Changes in version 1.13.2
+ Bug fix for importing DuplicationMetrics

Changes in version 1.13.1
+ Bug fixes for importing macs2 logs
+ Bug fixes for importing bowtie2 logs

Changes in version 1.9.3
+ Bug fixes for importing macs2 logs

Changes in version 1.9.2
+ Bug fixes for later versions of ggplot2

Changes in version 1.8.1
+ Bug fix in .makeSidebar

Changes in version 1.7.3
+ Simplifed version of plotFastqcPCA. Now groups are an optional factor. No clustering is performed

Changes in version 1.7.2
+ Deprecated runFastQC

Changes in version 1.7.1
+ Added macs2 callpeak logs to importNgsLogs

Changes in version 1.6.1
+ Added asPercent to plotAlignmentSummary
+ Added the ability to assign new values via fqName<-

Changes in version 1.5.5
+ Added importSJ for importing SJ.out.tab files from the aligner STAR

Changes in version 1.5.5
+ Added plotType = "residuals" for plotSeqContent()

Changes in version 1.5.4
+ Allowed for ignoring basename() calls in all importNgsLogs functions
+ Added cumulative GC plot to plotGcContent() as plotType = "cdf"
+ Changed plotting option name from cumulative to cdf for plotSeqLengthDistn()
+ Announced deprecation of runFastQC()

Changes in version 1.5.3
+ Fixed bug in plotOverrep

Changes in version 1.3.4
+ Fixed bug in cutadapt import

Changes in version 1.3.3
+ Added line plot to plotDupLevels()

Changes in version 1.3.2
+ Changed default template to use DT instead of kable for tables and removed kableExtra dependency
+ Added outputDir as an argument to writeHtmlReport()

Changes in version 1.1.4
+ added updated vignette

Changes in version 1.1.1
+ Added plotAlignmentSummary()
+ Added plotFastqcPCA()
+ Added quast, busco, cutadapt, featureCounts, trimmomatic, flagstats & AdapterRemoval support to importNgsLogs()
+ Enabled auto detection for report type for importNgsLogs()

Changes in version 1.0.2
+ Added Transcriptomic GC Content for A.thaliana to default gcTheoretical object

Changes in version 1.0.1
+ Table in default FastQC template now scroll for larger datasets
+ Kmers removed from default FastQC template
+ Typos in vignette corrected, seperate LICENSE file added & dplyr updates corrected
+ Corrected dependencies for writeHtmlReport

Changes in version 1.0.0
+ Initial Bioconductor release version

Changes in version 0.99.8 (2019-04-03)
+ **This is a breaking change!** Significant changes to most functions have been implemented
+ Extracting modules is no longer performed by individual functions, but is now performed using the function getModule
+ FastqcFileLists objects are no longer defined and the class FastqcFile has been made into the private class .FastqcFile
+ FastqcDataList objects have names attributes and can now be subset using names
+ The function fileName has been renamed as fqName to clarify that it refers to the underlying Fastq file for a Fastqc report
+ All log file imports are now handled by the single function importNgsLogs
+ Most plot functions have been renamed with shorter names, e.g. plotOverrepresentedSequences is now plotOverrep
+ The FastQC version is now obtained using fqcVersion not Version
+ The functions genomes() and transcriptomes() have been removed and this information is now obtained using gcAvail(object, type)
+ The function getGcDistn() has been renamed as estGcDistn() to avoid any confusion with getGC() which works on TheoreticalGC objects.

Changes in version 0.99.1 (2019-02-03)
+ Removed Remotes from DESCRIPTION
+ Added getGcDistribution to enable calculation of GC Content Distributions from FastaFiles

Changes in version 0.99.0 (2019-02-01)
+ Submitted to Bioconductor
+ Shiny App has been moved to a separate package, located at https://github.com/UofABioinformaticsHub/shinyNgsReports
