Package: CAFE 1.43.0

Sander Bollen

CAFE: Chromosmal Aberrations Finder in Expression data

Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input

Authors:Sander Bollen

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CAFE.pdf |CAFE.html✨
CAFE/json (API)
NEWS

# 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-1.43.0(bioc 3.21)CAFE-1.42.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpression microarray onechannel genesetenrichment

4.30 score 2 scripts 243 downloads 251 mentions 13 exports 158 dependencies

Last updated 23 days agofrom:da805c7be6. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win	WARNING	Nov 19 2024
R-4.5-linux	WARNING	Nov 19 2024
R-4.4-win	WARNING	Nov 19 2024
R-4.4-mac	WARNING	Nov 19 2024
R-4.3-win	WARNING	Nov 19 2024
R-4.3-mac	WARNING	Nov 19 2024

Exports:armStats bandStats chromosomeStats cliSubset discontPlot discontSmooth facetPlot fisher.method guiSubset ProcessCels rawPlot slidPlot slidSmooth

Dependencies:abind affy affyio annotate AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray dichromat digest dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome forcats foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GGally ggbio ggplot2 ggstats glue graph gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl OrganismDbi patchwork pillar pkgconfig plogr plyr png preprocessCore prettyunits progress ProtGenerics purrr R6 rappdirs RBGL RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 xtable XVector yaml zlibbioc

Manual

Rendered fromCAFE-manual.Rnwusingutils::Sweaveon Nov 19 2024.

Last update: 2014-03-20
Started: 2014-03-20

Citation

Development and contributors

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

Usage by other packages (reverse dependencies)