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