Package: ffpe 1.49.0

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

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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-1.49.0(bioc 3.20)ffpe-1.48.0(bioc 3.19)

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

bioconductor-package

3 exports 1.38 score 155 dependencies 2 mentions

Last updated 2 months agofrom:4e5607a117

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 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 RColorBrewer Rcpp RCurl readr reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales scrime 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

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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