Package: Cleanet 1.0.0

Cleanet: Automated Doublet Detection and Classification for Cytometry Data

Automated method for doublet detection in flow or mass cytometry data, based on simulating doublets and finding events whose protein expression patterns are similar to the simulated doublets.

Authors:Matei Ionita [aut, cre]

Cleanet_1.0.0.tar.gz
Cleanet_1.0.0.zip(r-4.7-x86_64)Cleanet_1.0.0.zip(r-4.7-arm64)Cleanet_1.0.0.zip(r-4.6-x86_64)Cleanet_1.0.0.zip(r-4.6-arm64)Cleanet_1.0.0.zip(r-4.5-x86_64)
Cleanet_1.0.0.tgz(r-4.6-x86_64)Cleanet_1.0.0.tgz(r-4.6-arm64)Cleanet_1.0.0.tgz(r-4.5-x86_64)Cleanet_1.0.0.tgz(r-4.5-arm64)
Cleanet_1.0.0.tar.gz(r-4.7-arm64)Cleanet_1.0.0.tar.gz(r-4.7-x86_64)Cleanet_1.0.0.tar.gz(r-4.6-arm64)Cleanet_1.0.0.tar.gz(r-4.6-x86_64)
Cleanet_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
Cleanet/json (API)

# Install 'Cleanet' in R:

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

Bug tracker:https://github.com/matei-ionita/cleanet/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

3.70 score 1 stars 1 scripts 268 downloads 6 exports 56 dependencies

Last updated from:d2532096d0. Checks:13 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	WARNING	175
linux-devel-x86_64	WARNING	213
source / vignettes	OK	240
linux-release-arm64	WARNING	182
linux-release-x86_64	WARNING	206
macos-release-arm64	WARNING	190
macos-release-x86_64	WARNING	521
macos-oldrel-arm64	WARNING	168
macos-oldrel-x86_64	WARNING	361
windows-devel-arm64	WARNING	404
windows-devel-x86_64	WARNING	220
windows-release-arm64	WARNING	398
windows-release-x86_64	WARNING	161
windows-oldrel-x86_64	WARNING	172
wasm-release	OK	200

Exports:add_doublet_parameter classify_doublets cleanet compare_doublets_exp_obs filter_debris_cytof filter_debris_flow

Dependencies:BH Biobase BiocGenerics biocmake bit bit64 cli clipr cpp11 crayon cytolib dir.expiry dplyr farver filelock flowCore generics ggplot2 glue gtable hms isoband labeling lifecycle magrittr matrixStats pillar pkgconfig plyr prettyunits progress purrr R6 RColorBrewer Rcpp RcppArmadillo RcppHNSW readr reshape2 Rhdf5lib rlang RProtoBufLib S4Vectors S7 scales stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr

Cleanet for Mass Cytometry

Rendered fromCleanet_for_mass_cytometry.Rmdusingknitr::rmarkdown

Last update: 2024-12-17
Started: 2024-12-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Classify doublets (or multiplets) based on component singlets.	classify_doublets
Detect doublets in a single cytometry sample	cleanet
Tabulate expected and observed proportions of doublet types.	compare_doublets_exp_obs
Flag debris in mass cytometry data.	filter_debris_cytof
Flag debris in flow cytometry data.	filter_debris_flow