TarSeqQC: TARgeted SEQuencing Experiment Quality Control

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.

AuthorGabriela A. Merino, Cristobal Fresno, Yanina Murua, Andrea S. Llera and Elmer A. Fernandez
Date of publicationNone
MaintainerGabriela Merino <gmerino@bdmg.com.ar>
LicenseGPL (>=2)
Version1.4.1
http://www.bdmg.com.ar

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

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