Changes in version 2.5.2 o Added `summariseOverrep()` Changes in version 2.5.1 o Changed method for setting default theme using plotTheme o Set factor levels for plotSeqContent for FastpDataList o Added line & cumulative plotTypes for plotInsertSize Changes in version 2.3.5 o added support for rnaseqc metrics files Changes in version 2.1.5 o Added FastpData and FastpDataList classes for working with fastp reports Changes in version 2.1.4 o Added umi_tools dedup to importNgsLogs Changes in version 2.1.3 o Bugfix when importing duplicationMetrics Changes in version 2.0.0 o Added status bar to all plots from FastQC reports using pachwork Changes in version 1.13.3 o Bug fix for importing macs2 logs Changes in version 1.13.2 o Bug fix for importing DuplicationMetrics Changes in version 1.13.1 o Bug fixes for importing macs2 logs o Bug fixes for importing bowtie2 logs Changes in version 1.9.3 o Bug fixes for importing macs2 logs Changes in version 1.9.2 o Bug fixes for later versions of ggplot2 Changes in version 1.8.1 o Bug fix in .makeSidebar Changes in version 1.7.3 o Simplifed version of plotFastqcPCA. Now groups are an optional factor. No clustering is performed Changes in version 1.7.2 o Deprecated runFastQC Changes in version 1.7.1 o Added macs2 callpeak logs to importNgsLogs Changes in version 1.6.1 o Added asPercent to plotAlignmentSummary o Added the ability to assign new values via fqName<- Changes in version 1.5.5 o Added importSJ for importing SJ.out.tab files from the aligner STAR o Added plotType = "residuals" for plotSeqContent() Changes in version 1.5.4 o Allowed for ignoring basename() calls in all importNgsLogs functions o Added cumulative GC plot to plotGcContent() as plotType = "cdf" o Changed plotting option name from cumulative to cdf for plotSeqLengthDistn() o Announced deprecation of runFastQC() Changes in version 1.5.3 o Fixed bug in plotOverrep Changes in version 1.3.4 o Fixed bug in cutadapt import Changes in version 1.3.3 o Added line plot to plotDupLevels() Changes in version 1.3.2 o Changed default template to use DT instead of kable for tables and removed kableExtra dependency o Added outputDir as an argument to writeHtmlReport() Changes in version 1.1.4 o added updated vignette Changes in version 1.1.1 o Added plotAlignmentSummary() o Added plotFastqcPCA() o Added quast, busco, cutadapt, featureCounts, trimmomatic, flagstats & AdapterRemoval support to importNgsLogs() o Enabled auto detection for report type for importNgsLogs() Changes in version 1.0.2 o Added Transcriptomic GC Content for A.thaliana to default gcTheoretical object Changes in version 1.0.1 o Table in default FastQC template now scroll for larger datasets o Kmers removed from default FastQC template o Typos in vignette corrected, seperate LICENSE file added & dplyr updates corrected o Corrected dependencies for writeHtmlReport Changes in version 1.0.0 o Initial Bioconductor release version Changes in version 0.99.8 (2019-04-03) o **This is a breaking change!** Significant changes to most functions have been implemented o Extracting modules is no longer performed by individual functions, but is now performed using the function getModule o FastqcFileLists objects are no longer defined and the class FastqcFile has been made into the private class .FastqcFile o FastqcDataList objects have names attributes and can now be subset using names o The function fileName has been renamed as fqName to clarify that it refers to the underlying Fastq file for a Fastqc report o All log file imports are now handled by the single function importNgsLogs o Most plot functions have been renamed with shorter names, e.g. plotOverrepresentedSequences is now plotOverrep o The FastQC version is now obtained using fqcVersion not Version o The functions genomes() and transcriptomes() have been removed and this information is now obtained using gcAvail(object, type) o 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) o Removed Remotes from DESCRIPTION o Added getGcDistribution to enable calculation of GC Content Distributions from FastaFiles Changes in version 0.99.0 (2019-02-01) o Submitted to Bioconductor o Shiny App has been moved to a separate package, located at https://github.com/UofABioinformaticsHub/shinyNgsReports