Package: ffpe 1.57.0

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_1.57.0.tar.gz
ffpe_1.57.0.zip(r-4.7)ffpe_1.57.0.zip(r-4.6)ffpe_1.57.0.zip(r-4.5)
ffpe_1.57.0.tgz(r-4.6-any)ffpe_1.57.0.tgz(r-4.5-any)
ffpe_1.57.0.tar.gz(r-4.7-any)ffpe_1.57.0.tar.gz(r-4.6-any)
ffpe_1.57.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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-1.57.0(bioc 3.24)ffpe-1.56.0(bioc 3.23)

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

microarray geneexpression qualitycontrol

4.13 score 34 scripts 484 downloads 2 mentions 3 exports 163 dependencies

Last updated from:d854178d4f. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	334
linux-devel-x86_64	NOTE	584
source / vignettes	OK	464
linux-release-x86_64	NOTE	602
macos-release-arm64	NOTE	264
macos-oldrel-arm64	NOTE	286
windows-devel	NOTE	458
windows-release	NOTE	498
windows-oldrel	NOTE	480
wasm-release	OK	289

Exports:CATplot sampleQC sortedIqrPlot

Dependencies:abind affy affyio annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry doRNG dplyr farver fastmap FDb.InfiniumMethylation.hg19 filelock foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable h5mread 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 nleqslv nlme nor1mix openssl org.Hs.eg.db pillar pkgconfig plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl readr rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors S7 scales scrime selectr Seqinfo 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 zoo

ffpe package user guide

Rendered fromffpe.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

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