Package: QDNAseq 1.41.0
Daoud Sie
QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations
Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.
Authors:
QDNAseq_1.41.0.tar.gz
QDNAseq_1.41.0.zip(r-4.5)QDNAseq_1.41.0.zip(r-4.4)QDNAseq_1.41.0.zip(r-4.3)
QDNAseq_1.41.0.tgz(r-4.4-any)QDNAseq_1.41.0.tgz(r-4.3-any)
QDNAseq_1.41.0.tar.gz(r-4.5-noble)QDNAseq_1.41.0.tar.gz(r-4.4-noble)
QDNAseq_1.41.0.tgz(r-4.4-emscripten)QDNAseq_1.41.0.tgz(r-4.3-emscripten)
QDNAseq.pdf |QDNAseq.html✨
QDNAseq/json (API)
NEWS
| # Install 'QDNAseq' in R: |
| install.packages('QDNAseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ccagc/qdnaseq/issues
- LGG150 - LGG150 chromosomes 7-10
On BioConductor:QDNAseq-1.41.0(bioc 3.20)QDNAseq-1.40.0(bioc 3.19)
Last updated 2 months agofrom:c25e2b94b3
Exports:addPhenodataapplyFiltersbinReadCountsbpendbpstartcalculateBlacklistcalculateBlacklistByRegionscalculateMappabilitycallBinschromosomescompareToReferencecorrectBinscreateBinsestimateCorrectionexportBinsfrequencyPlotgetBinAnnotationshighlightFiltersisobarPlotiterateResidualsmakeCghnoisePlotnormalizeBinsnormalizeSegmentedBinsplotpoolRunssegmentBinssmoothOutlierBins
Dependencies:askpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsCGHbaseCGHcallcodetoolscpp11crayoncurldigestDNAcopyformatRfutile.loggerfutile.optionsfuturefuture.applyGenomeInfoDbGenomeInfoDbDataGenomicRangesglobalshttrimputeIRangesjsonlitelambda.rlimmalistenvmarraymatrixStatsmimeopensslparallellyR.methodsS3R.ooR.utilsR6RhtslibRsamtoolsS4VectorssnowsnowfallstatmodsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Package QDNAseq | QDNAseq-package QDNAseq |
| Adds phenotype data from a file to a QDNAseqReadCounts or a QDNAseqCopyNumbers object | addPhenodata |
| Adjusts the filtering on which bins are used | applyFilters applyFilters,QDNAseqReadCounts-method |
| Calculate binned read counts from a set of BAM files | binReadCounts |
| Call aberrations from segmented copy number data | callBins callBins,QDNAseqCopyNumbers-method |
| Divide binned read counts with those of reference samples | compareToReference compareToReference,QDNAseqCopyNumbers,numeric-method |
| Correct binned read counts for GC content and mappability | correctBins correctBins,QDNAseqReadCounts-method |
| Builds bin annotation data for a particular bin size | calculateBlacklist calculateBlacklistByRegions calculateMappability createBins iterateResiduals |
| Estimate correction to read counts for GC content and mappability | estimateCorrection estimateCorrection,QDNAseqReadCounts-method |
| Exports to a file | exportBins exportBins,QDNAseqSignals-method |
| Plot copy number aberration frequencies | frequencyPlot frequencyPlot,QDNAseqCopyNumbers,missing-method |
| Gets bin annotation data for a particular bin size | getBinAnnotations |
| Highlights data points in a plotted profile to evaluate filtering | highlightFilters highlightFilters,QDNAseqSignals-method |
| Plot median read counts as a function of GC content and mappability | isobarPlot isobarPlot,QDNAseqReadCounts,missing-method |
| LGG150 chromosomes 7-10 | LGG150 |
| Constructs a 'cghRaw', 'cghSeg', or 'cghCall' object | makeCgh makeCgh,QDNAseqCopyNumbers-method |
| Plot noise as a function of sequence depth | noisePlot noisePlot,QDNAseqReadCounts,missing-method |
| Normalizes binned read counts | normalizeBins normalizeBins,QDNAseqCopyNumbers-method |
| Normalize segmented bins | normalizeSegmentedBins normalizeSegmentedBins,QDNAseqCopyNumbers-method |
| Plot copy number profile | plot plot,QDNAseqSignals,missing-method |
| Pools binned read counts across samples | poolRuns poolRuns,QDNAseqSignals,character-method |
| Defunct functions in package 'QDNAseq' | downloadBinAnnotations |
| Container for QDNAseq read count data | QDNAseqCopyNumbers QDNAseqCopyNumbers-class |
| Container for QDNAseq read count data | QDNAseqReadCounts QDNAseqReadCounts-class |
| A parent class for containers of QDNAseq data | bpend,QDNAseqSignals-method bpstart,QDNAseqSignals-method chromosomes,QDNAseqSignals-method QDNAseqSignals QDNAseqSignals-class |
| Segments normalized copy number data | segmentBins segmentBins,QDNAseqCopyNumbers-method |
| Smooth outlier bins after normalization | smoothOutlierBins smoothOutlierBins,QDNAseqCopyNumbers-method |
