TarSeqQC: TARgeted SEQuencing Experiment Quality Control

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The package allows the representation of targeted experiment in R. This is based on current packages and incorporates functions to do a quality control over this kind of experiments and a fast exploration of the sequenced regions. An xlsx file is generated as output.

Author
Gabriela A. Merino, Cristobal Fresno, Yanina Murua, Andrea S. Llera and Elmer A. Fernandez
Date of publication
None
Maintainer
Gabriela Merino <gmerino@bdmg.com.ar>
License
GPL (>=2)
Version
1.4.1
URLs

View on Bioconductor

Man pages

ampliPanel
An amplicon panel example for use the TarSeqQC R package.
ampliPanel2
An amplicon panel example for use the TarSeqQC R package.
checkBedFasta
Function to control Bed and FASTA files compatibility.
myCounts
A pileup matrix example for use the TarSeqQC R package.
object
A set of two amplicon panels example for use the TarSeqQC R...
pileupCounts
Function to obtain the pileup counts for a bam file.
plotInOutFeatures
Function to explore read percentages in targeted regions and...
TargetExperiment-biasExploration
Plot attribute density and boxplot for each bias source...
TargetExperiment-buildFeaturePanel
Function to build a feature panel based on specific genomic...
TargetExperiment-buildReport
TargetExperiment auxiliar function.
TargetExperiment-class
TargetExperiment S4 class implementation in R
TargetExperiment-constructor
TargetExperiment constructor
TargetExperiment-getters
Getters for TargetExperiment and TargetExperimentList...
TargetExperiment-initialize
TargetExperiment object constructor.
TargetExperimentList-class
TargetExperimentList S4 class implementation in R
TargetExperimentList-constructor
TargetExperimentList constructor
TargetExperimentList-initialize
TargetExperimentList object constructor.
TargetExperimentList-plotGlobalAttrExpl
Plot attribute exploration of a TargetExperimentList object.
TargetExperimentList-plotPoolPerformance
Plot pool performance of a TargetExperimentList object.
TargetExperiment-plot
Plot TargetExperiment object overview.
TargetExperiment-plotAttrExpl
Plot attribute exploration of a...
TargetExperiment-plotAttrPerform
Plot feature performance of a TargetExperiment object.
TargetExperiment-plotFeatPerform
Plot feature performance of a TargetExperiment object.
TargetExperiment-plotFeature
Plot read profiles for a particular feature.
TargetExperiment-plotGeneAttrPerFeat
Plot the attribute value for all the features of a selected...
TargetExperiment-plotMetaDataExpl
Graphical exploration of a specific metadata column.
TargetExperiment-plotNtdPercentage
Plot nucleotide read percentages for a particular feature.
TargetExperiment-plotRegion
Plot read profiles for a particular genomic region.
TargetExperiment-print
Print a TargetExperiment/TargetExperimentList object.
TargetExperiment-readFrequencies
Function to explore read frequencies in targeted regions and...
TargetExperiment-setters
Setters for the TargetExperiment slots
TargetExperiment-show
Show method for the TargetExperiment and TargetExperimentList...
TargetExperiment-statistics
TargetExperiment and TargetExperimentList summary methods.
TargetExperiment-summarizePanel
Function to summarize a featurePanel slot at a gene level.
TarSeqQC-package
TarSeqQC: Targeted Sequencing Experiment Quality Control R...
TEList
A set of two amplicon panels example for use the TarSeqQC R...

Files in this package

TarSeqQC/DESCRIPTION
TarSeqQC/NAMESPACE
TarSeqQC/NEWS
TarSeqQC/R
TarSeqQC/R/TarSeqQC-package.R
TarSeqQC/R/TargetExperiment-addStatSummSheet.R
TarSeqQC/R/TargetExperiment-ampliPanel.R
TarSeqQC/R/TargetExperiment-ampliPanel2.R
TarSeqQC/R/TargetExperiment-biasExploration.R
TarSeqQC/R/TargetExperiment-buildFeaturePanel.R
TarSeqQC/R/TargetExperiment-buildReport.R
TarSeqQC/R/TargetExperiment-constructor.R
TarSeqQC/R/TargetExperiment-getters.R
TarSeqQC/R/TargetExperiment-ggplotColours.R
TarSeqQC/R/TargetExperiment-initialize.R
TarSeqQC/R/TargetExperiment-myCounts.R
TarSeqQC/R/TargetExperiment-pileupCounts.R
TarSeqQC/R/TargetExperiment-plot.R
TarSeqQC/R/TargetExperiment-plotAttrExpl.R
TarSeqQC/R/TargetExperiment-plotAttrPerform.R
TarSeqQC/R/TargetExperiment-plotFeatPerform.R
TarSeqQC/R/TargetExperiment-plotFeature.R
TarSeqQC/R/TargetExperiment-plotGeneAttrPerFeat.R
TarSeqQC/R/TargetExperiment-plotInOutFeatures.R
TarSeqQC/R/TargetExperiment-plotMetaDataExpl.R
TarSeqQC/R/TargetExperiment-plotNtdPercentage.R
TarSeqQC/R/TargetExperiment-plotRegion.R
TarSeqQC/R/TargetExperiment-print.R
TarSeqQC/R/TargetExperiment-readFrequencies.R
TarSeqQC/R/TargetExperiment-setters.R
TarSeqQC/R/TargetExperiment-show.R
TarSeqQC/R/TargetExperiment-statistics.R
TarSeqQC/R/TargetExperiment-summarizePanel.R
TarSeqQC/R/TargetExperiment.R
TarSeqQC/R/TargetExperimentList-TEList.R
TarSeqQC/R/TargetExperimentList-constructor.R
TarSeqQC/R/TargetExperimentList-getters.R
TarSeqQC/R/TargetExperimentList-initialize.R
TarSeqQC/R/TargetExperimentList-plot.R
TarSeqQC/R/TargetExperimentList-plotAttrExpl.R
TarSeqQC/R/TargetExperimentList-plotGlobalAttrExpl.R
TarSeqQC/R/TargetExperimentList-plotPoolPerformance.R
TarSeqQC/R/TargetExperimentList-print.R
TarSeqQC/R/TargetExperimentList-setters.R
TarSeqQC/R/TargetExperimentList-show.R
TarSeqQC/R/TargetExperimentList-statistics.R
TarSeqQC/R/TargetExperimentList.R
TarSeqQC/R/checkBedFasta.R
TarSeqQC/build
TarSeqQC/build/vignette.rds
TarSeqQC/data
TarSeqQC/data/TEList.rda
TarSeqQC/data/ampliPanel.rda
TarSeqQC/data/ampliPanel2.rda
TarSeqQC/data/myCounts.rda
TarSeqQC/inst
TarSeqQC/inst/doc
TarSeqQC/inst/doc/TarSeqQC-vignette.R
TarSeqQC/inst/doc/TarSeqQC-vignette.Rnw
TarSeqQC/inst/doc/TarSeqQC-vignette.pdf
TarSeqQC/inst/extdata
TarSeqQC/inst/extdata/mybam.bam
TarSeqQC/inst/extdata/mybam.bam.bai
TarSeqQC/inst/extdata/mybed.bed
TarSeqQC/inst/extdata/myfasta.fa
TarSeqQC/inst/extdata/myfasta.fa.fai
TarSeqQC/inst/extdata/plot.pdf
TarSeqQC/inst/unitTests
TarSeqQC/inst/unitTests/test_TarSeqQC.R
TarSeqQC/man
TarSeqQC/man/TEList.Rd
TarSeqQC/man/TarSeqQC-package.Rd
TarSeqQC/man/TargetExperiment-biasExploration.Rd
TarSeqQC/man/TargetExperiment-buildFeaturePanel.Rd
TarSeqQC/man/TargetExperiment-buildReport.Rd
TarSeqQC/man/TargetExperiment-class.Rd
TarSeqQC/man/TargetExperiment-constructor.Rd
TarSeqQC/man/TargetExperiment-getters.Rd
TarSeqQC/man/TargetExperiment-initialize.Rd
TarSeqQC/man/TargetExperiment-plot.Rd
TarSeqQC/man/TargetExperiment-plotAttrExpl.Rd
TarSeqQC/man/TargetExperiment-plotAttrPerform.Rd
TarSeqQC/man/TargetExperiment-plotFeatPerform.Rd
TarSeqQC/man/TargetExperiment-plotFeature.Rd
TarSeqQC/man/TargetExperiment-plotGeneAttrPerFeat.Rd
TarSeqQC/man/TargetExperiment-plotMetaDataExpl.Rd
TarSeqQC/man/TargetExperiment-plotNtdPercentage.Rd
TarSeqQC/man/TargetExperiment-plotRegion.Rd
TarSeqQC/man/TargetExperiment-print.Rd
TarSeqQC/man/TargetExperiment-readFrequencies.Rd
TarSeqQC/man/TargetExperiment-setters.Rd
TarSeqQC/man/TargetExperiment-show.Rd
TarSeqQC/man/TargetExperiment-statistics.Rd
TarSeqQC/man/TargetExperiment-summarizePanel.Rd
TarSeqQC/man/TargetExperimentList-class.Rd
TarSeqQC/man/TargetExperimentList-constructor.Rd
TarSeqQC/man/TargetExperimentList-initialize.Rd
TarSeqQC/man/TargetExperimentList-plotGlobalAttrExpl.Rd
TarSeqQC/man/TargetExperimentList-plotPoolPerformance.Rd
TarSeqQC/man/ampliPanel.Rd
TarSeqQC/man/ampliPanel2.Rd
TarSeqQC/man/checkBedFasta.Rd
TarSeqQC/man/myCounts.Rd
TarSeqQC/man/object.Rd
TarSeqQC/man/pileupCounts.Rd
TarSeqQC/man/plotInOutFeatures.Rd
TarSeqQC/tests
TarSeqQC/tests/runTests.R
TarSeqQC/vignettes
TarSeqQC/vignettes/GlobalAttrPool.pdf
TarSeqQC/vignettes/NTDPercAMPL20.pdf
TarSeqQC/vignettes/RETRegion.pdf
TarSeqQC/vignettes/TEList.pdf
TarSeqQC/vignettes/TarSeqQC-vignette.Rnw
TarSeqQC/vignettes/TarSeqQCvignette.bib
TarSeqQC/vignettes/attrExpl.pdf
TarSeqQC/vignettes/attrPerfPool.pdf
TarSeqQC/vignettes/attrPerfPoolThres.pdf
TarSeqQC/vignettes/authblk.sty
TarSeqQC/vignettes/class.pdf
TarSeqQC/vignettes/coveragePerform.pdf
TarSeqQC/vignettes/featPerf.pdf
TarSeqQC/vignettes/featuregene7.pdf
TarSeqQC/vignettes/framed.sty
TarSeqQC/vignettes/gcExploration.pdf
TarSeqQC/vignettes/gene2Exploration.pdf
TarSeqQC/vignettes/gene4AttrFeat.pdf
TarSeqQC/vignettes/gene7Region.pdf
TarSeqQC/vignettes/geneAttrPerFeatOverlap.pdf
TarSeqQC/vignettes/geneExploration.pdf
TarSeqQC/vignettes/lengthExploration.pdf
TarSeqQC/vignettes/perfExplCCP.pdf
TarSeqQC/vignettes/plot.pdf
TarSeqQC/vignettes/plotCPP.pdf
TarSeqQC/vignettes/plotInOut.pdf
TarSeqQC/vignettes/plotNoLab.pdf
TarSeqQC/vignettes/plotTEList.pdf
TarSeqQC/vignettes/poolPerformDens.pdf
TarSeqQC/vignettes/poolPerformThres.pdf