Changes in version 2.2.1 + Improved plotting and parsing for FastpData and FastpDataList objects + Added the ability to hide PWF colours from most plots + Added the option of showing the legend in plotly line plots + Began passing ggplot2 scale and theme objects directly to Fastp and some Fastqc plotting functions + Added the pattern explicitly to most pltting functions 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