Load FastqQC reports and other NGS related files

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Documentation for package ‘ngsReports’ version 2.11.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

estGcDistn	Estimate a GC Content Distribution From Sequences
estGcDistn-method	Estimate a GC Content Distribution From Sequences
FastpData	The FastpData Object Class
FastpData-class	The FastpData Object Class
FastpDataList	The FastpDataList Object Class
FastpDataList-class	The FastpDataList Object Class
FastqcData	The FastqcData Object Class
FastqcData-class	The FastqcData Object Class
FastqcDataList	The FastqcDataList Object Class
FastqcDataList-class	The FastqcDataList Object Class
fqcVersion	Get the FASTQC version
fqcVersion-method	Get the FASTQC version
fqName	Return the Underlying Fastq File Names from Fastqc/Fastp Objects
fqName-method	Return the Underlying Fastq File Names from Fastqc/Fastp Objects
fqName<-	Return the Underlying Fastq File Names from Fastqc/Fastp Objects
fqName<--method	Return the Underlying Fastq File Names from Fastqc/Fastp Objects
gcAvail	List Genomes or Transcriptomes with Theoretical GC Content
gcAvail-method	List Genomes or Transcriptomes with Theoretical GC Content
gcTheoretical	Theoretical GC content
getColours	Work with objects of class PwfCols
getColours-method	Work with objects of class PwfCols
getGC	Get Theoretical GC content
getGC-method	Get Theoretical GC content
getModule	Retrieve a given module from a Fastqc* Object
getModule-method	Retrieve a given module from a Fastqc* Object
getSummary	Get the summary information from Fastqc Files
getSummary-method	Get the summary information from Fastqc Files
importNgsLogs	Import Various NGS-related log files
importSJ	Import STAR Splice Junctions
isCompressed	Check to see if a file is compressed
maxAdapterContent	Get the maximum Adapter Content
mData	Extract Metadata for TheoreticalGC objects
mData-method	Extract Metadata for TheoreticalGC objects
overRep2Fasta	Write fasta of Over-Represented sequences.
overRep2Fasta-method	Write fasta of Over-Represented sequences.
path	Return the File Paths from an object
path-method	Return the File Paths from an object
plotAdapterContent	Draw an Adapter Content Plot
plotAdapterContent-method	Draw an Adapter Content Plot
plotAlignmentSummary	Plot a summary of alignments
plotAssemblyStats	Plot a summary of assembly logs
plotBaseQuals	Plot the Base Qualities for each file
plotBaseQuals-method	Plot the Base Qualities for each file
plotDupLevels	Plot the combined Sequence_Duplication_Levels information
plotDupLevels-method	Plot the combined Sequence_Duplication_Levels information
plotFastqcPCA	Draw a PCA plot for Fast QC modules
plotFastqcPCA-method	Draw a PCA plot for Fast QC modules
plotGcContent	Plot the Per Sequence GC Content
plotGcContent-method	Plot the Per Sequence GC Content
plotInsertSize	Plot Insert Size Distributions
plotInsertSize-method	Plot Insert Size Distributions
plotKmers	Plot Overrepresented Kmers
plotKmers-method	Plot Overrepresented Kmers
plotNContent	Draw an N Content Plot
plotNContent-method	Draw an N Content Plot
plotOverrep	Plot a summary of Over-represented Sequences
plotOverrep-method	Plot a summary of Over-represented Sequences
plotReadTotals	Draw a barplot of read totals
plotReadTotals-method	Draw a barplot of read totals
plotSeqContent	Plot the per base content as a heatmap
plotSeqContent-method	Plot the per base content as a heatmap
plotSeqLengthDistn	Plot the Sequence Length Distribution
plotSeqLengthDistn-method	Plot the Sequence Length Distribution
plotSeqQuals	Plot the Per Sequence Quality Scores
plotSeqQuals-method	Plot the Per Sequence Quality Scores
plotSummary	Plot the PASS/WARN/FAIL information
plotSummary-method	Plot the PASS/WARN/FAIL information
pwf	Colours for PASS/WARN/FAIL
PwfCols	The PwfCols class and associated methods
PwfCols-class	The PwfCols class and associated methods
readTotals	Get the read totals
setAlpha	Work with objects of class PwfCols
setAlpha-method	Work with objects of class PwfCols
setColours	Work with objects of class PwfCols
setColours-method	Work with objects of class PwfCols
summariseOverrep	Summarise Overrepresented Sequences
summariseOverrep-method	Summarise Overrepresented Sequences
TheoreticalGC-class	The TheoreticalGC Object Class
writeHtmlReport	Write an HTML Summary Report
[-method	Extract Elements