Man pages for UofABioinformaticsHub/fastqcReports
Load FastqQC reports and other NGS related files

dot-addPercentAdd a percentage sign
dot-emptyPlotCreate an empty plot with supplied text
dot-FastqcFile-classThe .FastqcFile Object Class
dot-getToolNameIdentify tool name
dot-hidePWFRectsHide PWF tooltips from line plots
dot-isValidAdapterRemovalLogCheck for a valid AdapterRemoval log
dot-isValidBowtieLogCheck for correct structure of supplied Bowtie log files
dot-isValidBuscoLogCheck for correct structure of supplied BUSCO log files
dot-isValidCutadaptLogCheck for a valid cutadapt log
dot-isValidDuplicationMetricsLogCheck for a valid Duplication Metrics log
dot-isValidFeatureCountsLogCheck for a valid featureCounts Summary
dot-isValidFlagstatLogCheck for correct structure of supplied flagstat
dot-isValidHisat2LogCheck for a valid Hisat2 log
dot-isValidQuastLogCheck for correct structure of supplied Quast log files
dot-isValidStarLogCheck for a valid Star Alignment log
dot-isValidTrimmomaticLogCheck for correct structure of supplied Trimmomatic log files
dot-makeDendroMake the dendrogram for heatmap-style plots
dot-makeLabelsPerform the checks and return the labels
dot-makeSidebarShortcut for making the status sidebar
dot-parseAdapterRemovalLogsParse data from Adapter Removal log files
dot-parseBowtieLogsParse data from Bowtie log files
dot-parseBuscoLogsParse data from BUSCO log files
dot-parseCutadaptLogsParse data from cutadapt log files
dot-parseDuplicationMetricsLogsParse data from Picard duplicationMetrics log files
dot-parseFeatureCountsLogsParse data from featureCounts summary files
dot-parseFlagstatLogsParse data from samtools flagstat files
dot-parseHisat2LogsParse data from HISAT2 log files
dot-parseQuastLogsParse data from BUSCO log files
dot-parseStarLogsParse data from STAR log files
dot-parseTrimmomaticLogsParse data from trimmomatic log files
dot-renderDendroSet up dendrograms for interactive plots
dot-scale_fill_pwfConstruct a scale using PwfCols
dot-splitByTabSplit elements of a vector into a data.frame
estGcDistnEstimate a GC Content Distribution From Sequences
extract-methodsExtract Elements
FastqcDataThe FastqcData Object Class
FastqcDataListThe FastqcDataList Object Class
fqcVersionGet the FASTQC version
fqName-methodsReturn the Underlying Fastq File Names from FastqcData*...
gcAvailList Genomes or Transcriptomes with Theoretical GC Content
gcTheoreticalTheoretical GC content
getColours-methodsWork with objects of class PwfCols
getGCGet Theoretical GC content
getModuleRetrieve a given module from a Fastqc* Object
getSummaryGet the summary information from Fastqc Files
importNgsLogsImport Various NGS-related log files
importSJImport STAR Splice Junctions
isCompressedCheck to see if a file is compressed
maxAdapterContentGet the maximum Adapter Content
mDataExtract Metadata for TheoreticalGC objects
overRep2Fasta-methodsWrite fasta of Over-Represented sequences.
pathReturn the File Paths from an object
plotAdapterContent-methodsDraw an Adapter Content Plot
plotAlignmentSummaryPlot a summary of alignments
plotAssemblyStatsPlot a summary of assembly logs
plotBaseQuals-methodsPlot the Base Qualities for each file
plotDupLevels-methodsPlot the combined Sequence_Duplication_Levels information
plotFastqcPCA-methodsDraw a PCA plot for Fast QC modules
plotGcContent-methodsPlot the Per Sequence GC Content
plotKmers-methodsPlot Overrepresented Kmers
plotNContent-methodsDraw an N Content Plot
plotOverrep-methodsPlot a summary of Over-represented Sequences
plotReadTotals-methodsDraw a barplot of read totals
plotSeqContent-methodsPlot the per base content as a heatmap
plotSeqLengthDistn-methodsPlot the Sequence Length Distribution
plotSeqQuals-methodsPlot the Per Sequence Quality Scores
plotSummary-methodsPlot the PASS/WARN/FAIL information
pwfColours for PASS/WARN/FAIL
PwfCols-classThe PwfCols class and associated methods
readTotalsGet the read totals
runFastQC-methodsA wrapper for the bash shell command fastqc.
TheoreticalGC-classThe TheoreticalGC Object Class
writeHtmlReportWrite an HTML Summary Report
UofABioinformaticsHub/fastqcReports documentation built on Nov. 21, 2020, 7:44 p.m.