Package: Rqc 1.39.0

Welliton Souza

Rqc: Quality Control Tool for High-Throughput Sequencing Data

Rqc is an optimised tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.

Authors:Welliton Souza, Benilton Carvalho <[email protected]>

Rqc_1.39.0.tar.gz
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Rqc.pdf |Rqc.html✨
Rqc/json (API)
NEWS

# Install 'Rqc' in R:

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

Bug tracker:https://github.com/labbcb/rqc/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:Rqc-1.39.0(bioc 3.20)Rqc-1.38.0(bioc 3.19)

bioconductor-package

43 exports 0.91 score 149 dependencies 3 mentions

Last updated 2 months agofrom:72371069db

Exports:checkpoint detectFileFormat fromRRDNA matdist perCycleBasecall perCycleQuality perFileInformation perFileTopReads perReadFrequency perReadQuality perReadWidth rqc rqcCycleAverageQualityCalc rqcCycleAverageQualityPcaCalc rqcCycleAverageQualityPcaPlot rqcCycleAverageQualityPlot rqcCycleBaseCallsCalc rqcCycleBaseCallsLinePlot rqcCycleBaseCallsPlot rqcCycleGCCalc rqcCycleGCPlot rqcCycleQualityBoxCalc rqcCycleQualityBoxPlot rqcCycleQualityCalc rqcCycleQualityPlot rqcFileHeatmap rqcGroupCycleAverageQualityCalc rqcGroupCycleAverageQualityPlot rqcQA rqcReadFrequencyCalc rqcReadFrequencyPlot rqcReadQualityBoxCalc rqcReadQualityBoxPlot rqcReadQualityCalc rqcReadQualityPlot rqcReadWidthCalc rqcReadWidthPlot rqcReport rqcShinyReport stats4trim subsetByGroup subsetByPair toRRDNA

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocGenerics BiocIO BiocManager BiocParallel BiocStyle Biostrings biovizBase bit bit64 bitops blob bookdown BSgenome bslib cachem checkmate cli cluster codetools colorspace commonmark cpp11 crayon curl data.table DBI DelayedArray deldir dichromat digest ensembldb evaluate fansi farver fastmap fontawesome foreign formatR Formula fs futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges ggplot2 glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httpuv httr hwriter interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr plyr png promises ProtGenerics pwalign R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales shiny ShortRead snow sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xtable XVector yaml zlibbioc

Rqc - Quality Control Tool for High-Throughput Sequencing Data

Welliton Souza, Benilton Carvalho

Rendered fromRqc.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2019-03-01
Started: 2014-10-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Quality Control Tool for High-Throughput Sequencing Data	Rqc-package Rqc
Save time storing longer analysis step on disk	checkpoint
Detect file format	detectFileFormat
Revert codified DNA sequences to original DNA sequences.	fromRRDNA
Distance matrix of the similarity between the DNA sequences.	matdist
Main Rqc function	rqc
Per cycle average quality by files	rqcCycleAverageQualityCalc rqcCycleAverageQualityPlot
Biplot of PCA of per cycle read average quality	rqcCycleAverageQualityPcaCalc rqcCycleAverageQualityPcaPlot
Per cycle base calls plot	rqcCycleBaseCallsCalc rqcCycleBaseCallsLinePlot rqcCycleBaseCallsPlot
Per cycle percentual GC plot	rqcCycleGCCalc rqcCycleGCPlot
Per cycle quality box plot	rqcCycleQualityBoxCalc rqcCycleQualityBoxPlot
Per cycle quality plot	rqcCycleQualityCalc rqcCycleQualityPlot
Heatmap of distance matrix of top over-represented reads	rqcFileHeatmap
Per group average quality across cycles	rqcGroupCycleAverageQualityCalc rqcGroupCycleAverageQualityPlot
Quality Assessment Rqc function	rqcQA rqcQA,BamFile-method rqcQA,character-method rqcQA,FastqFile-method rqcQA,list-method
Read frequency plot	rqcReadFrequencyCalc rqcReadFrequencyPlot
Per read mean quality box plot	rqcReadQualityBoxCalc rqcReadQualityBoxPlot
Per read quality plot	rqcReadQualityCalc rqcReadQualityPlot
Per read width plot	rqcReadWidthCalc rqcReadWidthPlot
Quality Control HTML Report	rqcReport
Class RqcResultSet	perCycleBasecall perCycleBasecall,list-method perCycleBasecall,RqcResultSet-method perCycleQuality perCycleQuality,list-method perCycleQuality,RqcResultSet-method perFileInformation perFileInformation,list-method perFileInformation,RqcResultSet-method perFileTopReads perFileTopReads,list-method perFileTopReads,RqcResultSet-method perReadFrequency perReadFrequency,list-method perReadFrequency,RqcResultSet-method perReadQuality perReadQuality,list-method perReadQuality,RqcResultSet-method perReadWidth perReadWidth,list-method perReadWidth,RqcResultSet-method RqcResultSet-class
Interactive Quality Control Report	rqcShinyReport
Minimun read mean quality and maximum percentage loss of reads estimations for trimming step.	stats4trim
Subset RqcResultSet object by group name.	subsetByGroup
Subset RqcResultSet object by pair files.	subsetByPair
Title: Convert DNA sequences to Reduced Representation format	toRRDNA