NEWS
ngsReports 2.5.2
- Added 'summariseOverrep()'
ngsReports 2.5.1
- Changed method for setting default theme using plotTheme
- Set factor levels for plotSeqContent for FastpDataList
- Added line & cumulative plotTypes for plotInsertSize
ngsReports 2.3.5
- added support for rnaseqc metrics files
ngsReports 2.1.5
- Added FastpData and FastpDataList classes for working with fastp reports
ngsReports 2.1.4
- Added umi_tools dedup to importNgsLogs
ngsReports 2.1.3
- Bugfix when importing duplicationMetrics
ngsReports 2.0.0
- Added status bar to all plots from FastQC reports using pachwork
ngsReports 1.13.3
- Bug fix for importing macs2 logs
ngsReports 1.13.2
- Bug fix for importing DuplicationMetrics
ngsReports 1.13.1
- Bug fixes for importing macs2 logs
- Bug fixes for importing bowtie2 logs
ngsReports 1.9.3
- Bug fixes for importing macs2 logs
ngsReports 1.9.2
- Bug fixes for later versions of ggplot2
ngsReports 1.8.1
ngsReports 1.7.3
- Simplifed version of plotFastqcPCA. Now groups are an optional factor. No clustering is performed
ngsReports 1.7.2
ngsReports 1.7.1
- Added macs2 callpeak logs to importNgsLogs
ngsReports 1.6.1
- Added asPercent to plotAlignmentSummary
- Added the ability to assign new values via fqName<-
ngsReports 1.5.5
- Added importSJ for importing SJ.out.tab files from the aligner STAR
- Added plotType = "residuals" for plotSeqContent()
ngsReports 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()
ngsReports 1.5.3
ngsReports 1.3.4
- Fixed bug in cutadapt import
ngsReports 1.3.3
- Added line plot to plotDupLevels()
ngsReports 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()
ngsReports 1.1.4
ngsReports 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()
ngsReports 1.0.2
- Added Transcriptomic GC Content for A.thaliana to default gcTheoretical object
ngsReports 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
ngsReports 1.0.0
- Initial Bioconductor release version
ngsReports 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.
ngsReports 0.99.1 (2019-02-03)
- Removed Remotes from DESCRIPTION
- Added getGcDistribution to enable calculation of GC Content Distributions from FastaFiles
ngsReports 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