Package: quantsmooth 1.79.0
Jan Oosting
quantsmooth: Quantile smoothing and genomic visualization of array data
Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53.
Authors:
quantsmooth_1.79.0.tar.gz
quantsmooth_1.79.0.zip(r-4.7)quantsmooth_1.79.0.zip(r-4.6)quantsmooth_1.79.0.zip(r-4.5)
quantsmooth_1.79.0.tgz(r-4.6-any)quantsmooth_1.79.0.tgz(r-4.5-any)
quantsmooth_1.79.0.tar.gz(r-4.7-any)quantsmooth_1.79.0.tar.gz(r-4.6-any)
quantsmooth_1.79.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
quantsmooth/json (API)
| # Install 'quantsmooth' in R: |
| install.packages('quantsmooth', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- affy.cn - Example data from several quantitative genomic methods
- affy.pos - Example data from several quantitative genomic methods
- bac.cn - Example data from several quantitative genomic methods
- bac.pos - Example data from several quantitative genomic methods
- chrom.bands - Dataset of human chromosomes and their banding patterns
- chrom.bands.hg18 - Dataset of human chromosomes and their banding patterns
- chrom.bands.hg19 - Dataset of human chromosomes and their banding patterns
- chrom.bands.hg38 - Dataset of human chromosomes and their banding patterns
- chrom.bands.mm10 - Dataset of human chromosomes and their banding patterns
- ill.cn - Example data from several quantitative genomic methods
- ill.pos - Example data from several quantitative genomic methods
On BioConductor:quantsmooth-1.79.0(bioc 3.24)quantsmooth-1.78.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
visualizationcopynumbervariation
Last updated from:a4249466a7. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 160 | ||
| linux-devel-x86_64 | NOTE | 157 | ||
| source / vignettes | OK | 138 | ||
| linux-release-x86_64 | NOTE | 183 | ||
| macos-release-arm64 | NOTE | 97 | ||
| macos-oldrel-arm64 | NOTE | 87 | ||
| windows-devel | NOTE | 90 | ||
| windows-release | NOTE | 98 | ||
| windows-oldrel | NOTE | 89 | ||
| wasm-release | OK | 90 |
Exports:characterCHRdrawSimpleChromgetChangedIdxgetChangedRegionsgetLambdaMingrid.chromosomelengthChromosomenumericCHRpaintCytobandsplotChromosomeplotSmoothedposition2CytobandprepareGenomePlotquantsmoothquantsmooth.cvquantsmooth.segscaleto
Dependencies:latticeMASSMatrixMatrixModelsquantregSparseMsurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Dataset of human chromosomes and their banding patterns | chrom.bands chrom.bands.hg18 chrom.bands.hg19 chrom.bands.hg38 chrom.bands.mm10 |
| Example data from several quantitative genomic methods | affy.cn affy.pos bac.cn bac.pos chr14 ill.cn ill.pos |
| Draw chromosome-like icons | drawSimpleChrom |
| getChangedRegions | getChangedRegions |
| getLambdaMin | getLambdaMin |
| Draw a chromosome using the grid package | grid.chromosome |
| Retrieve chromosomal length | lengthChromosome |
| Conversion of chromosome IDs between numeric and character | characterCHR numericCHR |
| Paint a chromosomal idiogram | paintCytobands |
| Wrapper for plotSmoothed | plotChromosome |
| plotSmoothed | plotSmoothed |
| Determine cytoband position based on location of probe | position2Cytoband |
| Set up a full genome plot | prepareGenomePlot |
| quantsmooth | quantsmooth |
| quantsmooth.cv | quantsmooth.cv |
| quantsmooth.seg | quantsmooth.seg |
| Scales data within a range to a new range | scaleto |
