Package: ngsReports 2.9.0

Stevie Pederson

ngsReports: Load FastqQC reports and other NGS related files

This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into R. As well as parsing files, multiple plotting methods have been implemented for visualising the parsed data. Plots can be generated as static ggplot objects or interactive plotly objects.

Authors:Stevie Pederson [aut, cre], Christopher Ward [aut], Thu-Hien To [aut]

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ngsReports.pdf |ngsReports.html✨
ngsReports/json (API)
NEWS

# Install 'ngsReports' in R:

install.packages('ngsReports', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/smped/ngsreports/issues

Datasets:

gcTheoretical - Theoretical GC content

On BioConductor:ngsReports-2.9.0(bioc 3.21)ngsReports-2.8.0(bioc 3.20)

qualitycontrol reportwriting

8.19 score 22 stars 98 scripts 233 downloads 3 mentions 42 exports 90 dependencies

Last updated 19 days agofrom:eb02955c95. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 14 2024
R-4.5-win	WARNING	Nov 14 2024
R-4.5-linux	WARNING	Nov 14 2024
R-4.4-win	WARNING	Nov 14 2024
R-4.4-mac	WARNING	Nov 14 2024
R-4.3-win	WARNING	Nov 14 2024
R-4.3-mac	WARNING	Nov 14 2024

Exports:estGcDistn FastpData FastpDataList FastqcData FastqcDataList fqcVersion fqName fqName<-gcAvail getColours getGC getModule getSummary importNgsLogs importSJ isCompressed maxAdapterContent mData overRep2Fasta path plotAdapterContent plotAlignmentSummary plotAssemblyStats plotBaseQuals plotDupLevels plotFastqcPCA plotGcContent plotInsertSize plotKmers plotNContent plotOverrep plotReadTotals plotSeqContent plotSeqLengthDistn plotSeqQuals plotSummary pwf readTotals setAlpha setColours summariseOverrep writeHtmlReport

Dependencies:askpass backports base64enc BiocGenerics Biostrings bslib cachem checkmate cli colorspace cpp11 crayon crosstalk curl data.table digest dplyr evaluate fansi farver fastmap fontawesome forcats fs generics GenomeInfoDb GenomeInfoDbData ggdendro ggplot2 glue gtable highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lubridate magrittr MASS Matrix memoise mgcv mime munsell nlme openssl patchwork pillar pkgconfig plotly plyr promises purrr R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown S4Vectors sass scales stringi stringr sys tibble tidyr tidyselect timechange tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc zoo

An Introduction To ngsReports

Christopher Ward, Hien To, Stevie Pederson

Rendered fromngsReportsIntroduction.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2023-04-14
Started: 2017-10-04

Citation

Development and contributors

Readme and manuals

Help Manual

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