1 Introduction | 2 Analysis | 3 In a nutshell | 4 Behind the scenes | 5 References
Package: CAFE 1.49.0
Sander Bollen
CAFE: Chromosmal Aberrations Finder in Expression data
Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input
Authors:
CAFE_1.49.0.tar.gz
CAFE_1.49.0.zip(r-4.7-any)CAFE_1.49.0.zip(r-4.6-any)CAFE_1.49.0.zip(r-4.5-any)
CAFE_1.49.0.tgz(r-4.6-any)CAFE_1.49.0.tgz(r-4.5-any)
CAFE_1.49.0.tar.gz(r-4.7-any)CAFE_1.49.0.tar.gz(r-4.6-any)
CAFE_1.49.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CAFE/json (API)
| # Install 'CAFE' in R: |
| install.packages('CAFE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- CAFE_data - CAFE data set
On BioConductor:CAFE-1.49.0(bioc 3.24)CAFE-1.48.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneexpressionmicroarrayonechannelgenesetenrichment
Last updated from:01db6cd436. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 251 | ||
| linux-devel-x86_64 | WARNING | 534 | ||
| source / vignettes | OK | 393 | ||
| linux-release-x86_64 | WARNING | 513 | ||
| macos-release-arm64 | WARNING | 245 | ||
| macos-oldrel-arm64 | WARNING | 391 | ||
| windows-devel | WARNING | 335 | ||
| windows-release | WARNING | 386 | ||
| windows-oldrel | WARNING | 365 | ||
| wasm-release | OK | 193 |
Exports:armStatsbandStatschromosomeStatscliSubsetdiscontPlotdiscontSmoothfacetPlotfisher.methodguiSubsetProcessCelsrawPlotslidPlotslidSmooth
Dependencies:abindaffyaffyioannotateAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestensembldbevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggbioggplot2gluegraphgridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslOrganismDbipkgconfigplyrpngpreprocessCoreProtGenericsR6rappdirsRBGLRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Chromosomal Aberrations Finder in Expression data | CAFE-package CAFE |
| Find aberrations with chromosome arm resolution | armStats |
| Find aberrations with cytoband resolution | bandStats |
| CAFE data set | CAFE_data |
| Find aberrations with whole-chromosome resolution | chromosomeStats |
| Subset data with a CLI | cliSubset |
| Plot with discontinuous smoother | discontPlot |
| A discontinuous smoother | discontSmooth |
| Plot all chromosomes horizontally next to each other | facetPlot |
| Combines pvalues by using Fisher's method | fisher.method |
| Subset data with a GUI | guiSubset |
| Processing CEL files | ProcessCels |
| Plot without any smoother | rawPlot |
| Plot with sliding average smoother | slidPlot |
| A moving average smoother | slidSmooth |