Package: PeacoQC 1.22.0

Annelies Emmaneel

PeacoQC: Peak-based selection of high quality cytometry data

This is a package that includes pre-processing and quality control functions that can remove margin events, compensate and transform the data and that will use PeacoQCSignalStability for quality control. This last function will first detect peaks in each channel of the flowframe. It will remove anomalies based on the IsolationTree function and the MAD outlier detection method. This package can be used for both flow- and mass cytometry data.

Authors:Annelies Emmaneel [aut, cre]

PeacoQC_1.22.0.tar.gz
PeacoQC_1.22.0.zip(r-4.7)PeacoQC_1.22.0.zip(r-4.6)PeacoQC_1.22.0.zip(r-4.5)
PeacoQC_1.22.0.tgz(r-4.6-any)PeacoQC_1.22.0.tgz(r-4.5-any)
PeacoQC_1.22.0.tar.gz(r-4.7-any)PeacoQC_1.22.0.tar.gz(r-4.6-any)
PeacoQC_1.22.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PeacoQC/json (API)

# Install 'PeacoQC' in R:

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

Bug tracker:https://github.com/saeyslab/peacoqc/issues

On BioConductor:PeacoQC-1.23.0(bioc 3.24)PeacoQC-1.22.0(bioc 3.23)

flowcytometry qualitycontrol preprocessing peakdetection

8.36 score 21 stars 4 packages 57 scripts 5 exports 72 dependencies

Last updated from:b86dec8d49 (on RELEASE_3_23). Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	166
linux-devel-x86_64	WARNING	278
source / vignettes	OK	249
linux-release-x86_64	WARNING	254
macos-release-arm64	WARNING	168
macos-oldrel-arm64	WARNING	140
windows-devel	WARNING	174
windows-release	WARNING	184
windows-oldrel	WARNING	160
wasm-release	OK	174

Exports:PeacoQC PeacoQCHeatmap PlotPeacoQC RemoveDoublets RemoveMargins

Dependencies:abind BH Biobase BiocGenerics biocmake circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon cytolib data.table DelayedArray digest dir.expiry doParallel dplyr farver filelock flowCore flowWorkspace foreach generics GetoptLong ggplot2 GlobalOptions glue graph gridExtra gtable IRanges isoband iterators labeling lattice lifecycle magrittr Matrix MatrixGenerics matrixStats ncdfFlow pillar pkgconfig plyr png R6 RBGL RColorBrewer Rcpp Rgraphviz Rhdf5lib rjson rlang RProtoBufLib S4Arrays S4Vectors S7 scales shape SparseArray tibble tidyselect utf8 vctrs viridisLite withr XML XVector

PeacoQC

Rendered fromPeacoQC_Vignette.Rmdusingknitr::rmarkdown

Last update: 2022-12-16
Started: 2020-01-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Peak-based detection of high quality cytometry data	PeacoQC
Make overview heatmap of quality control analysis	PeacoQCHeatmap
Visualise deleted cells of PeacoQC	PlotPeacoQC
Remove doublet events from flow cytometry data	RemoveDoublets
Remove margin events of flow cytometry data	RemoveMargins