Package: ffpe 1.51.0

Levi Waldron

ffpe: Quality assessment and control for FFPE microarray expression data

Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

Authors:Levi Waldron

ffpe_1.51.0.tar.gz
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ffpe.pdf |ffpe.html✨
ffpe/json (API)

# Install 'ffpe' in R:

install.packages('ffpe', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:ffpe-1.51.0(bioc 3.21)ffpe-1.50.0(bioc 3.20)

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

microarray geneexpression qualitycontrol

3.03 score 27 scripts 252 downloads 2 mentions 3 exports 160 dependencies

Last updated 2 months agofrom:a03eb8251d. Checks:ERROR: 2 WARNING: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	ERROR	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	WARNING	Oct 31 2024

Exports:CATplot sampleQC sortedIqrPlot

Dependencies:abind affy affyio annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cli clipr codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest doRNG dplyr fansi farver fastmap FDb.InfiniumMethylation.hg19 foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable HDF5Array hms httr httr2 illuminaio IRanges isoband iterators jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle limma locfit lumi magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mgcv mime minfi multtest munsell nleqslv nlme nor1mix openssl org.Hs.eg.db pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors scales scrime selectr sfsmisc siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect TTR TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xml2 xtable xts XVector yaml zlibbioc zoo

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Quality assessment and control for FFPE microarray expression data	ffpe-package ffpe
Make a Concordance at the Top plot.	CATplot
Sample quality control for FFPE expression data	sampleQC sampleQC,AffyBatch-method sampleQC,LumiBatch-method sampleQC,matrix-method sampleQC-method
Minimal box plot of samples, which get ordered optionally by batch, then by IQR.	sortedIqrPlot sortedIqrPlot,AffyBatch-method sortedIqrPlot,LumiBatch-method sortedIqrPlot,matrix-method