Package: Polytect 1.5.0

Yao Chen

Polytect: An R package for digital data clustering

Polytect is an advanced computational tool designed for the analysis of multi-color digital PCR data. It provides automatic clustering and labeling of partitions into distinct groups based on clusters first identified by the flowPeaks algorithm. Polytect is particularly useful for researchers in molecular biology and bioinformatics, enabling them to gain deeper insights into their experimental results through precise partition classification and data visualization.

Authors:Yao Chen [aut, cre]

Polytect_1.5.0.tar.gz
Polytect_1.5.0.zip(r-4.7)Polytect_1.5.0.zip(r-4.6)Polytect_1.5.0.zip(r-4.5)
Polytect_1.5.0.tgz(r-4.6-any)Polytect_1.5.0.tgz(r-4.5-any)
Polytect_1.5.0.tar.gz(r-4.7-any)Polytect_1.5.0.tar.gz(r-4.6-any)
Polytect_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Polytect/json (API)

# Install 'Polytect' in R:

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

Bug tracker:https://github.com/emmachenlingo/polytect/issues

Datasets:

BPV - BPV data
CA - CA data
CNV5plex - CNV 5-plex data
CNV6plex - CNV 6-plex data
HIV - HIV data
HR - HR data
LR - LR data
MM - MM data

On BioConductor:Polytect-1.5.0(bioc 3.24)Polytect-1.4.0(bioc 3.23)

ddpcr clustering multichannel classification

4.00 score 1 stars 4 scripts 6 exports 128 dependencies

Last updated from:48dacdd5c2. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	196
linux-devel-x86_64	NOTE	293
source / vignettes	OK	317
linux-release-x86_64	NOTE	286
macos-release-arm64	NOTE	140
macos-oldrel-arm64	NOTE	197
windows-devel	NOTE	165
windows-release	NOTE	180
windows-oldrel	NOTE	184
wasm-release	OK	247

Exports:conc_cal polytect_clust polytect_merge polytect_plot polytect_summary sil_plot

Dependencies:askpass backports base64enc BBmisc BiocManager bit bit64 blob broom bslib cachem callr cellranger checkmate cli clipr conflicted cowplot cpp11 crayon curl data.table DBI dbplyr DiceKriging digest dplyr dtplyr evaluate farver fastmap fastmatch flowPeaks fontawesome forcats fs gargle generics ggplot2 glue googledrive googlesheets4 gtable haven highr hms htmltools httr ids isoband jquerylib jsonlite knitr labeling lattice lhs lifecycle lubridate magrittr MASS Matrix MatrixModels memoise mime mlr mlrMBO mnormt modelr mvtnorm numDeriv openssl otel parallelMap ParamHelpers pillar pkgconfig prettyunits processx progress ps purrr quantreg R6 ragg rappdirs RColorBrewer Rcpp RcppArmadillo readr readxl rematch rematch2 reprex rgenoud rlang rmarkdown rstudioapi rvest S7 sass scales selectr smoof sn SparseM stringi stringr survival sys systemfonts textshaping tibble tidyr tidyselect tidyverse timechange tinytex tzdb utf8 uuid vctrs viridisLite vroom withr xfun XML xml2 yaml

A guide to use the Polytect: an automatic clustering and labeling method for multi-color digital PCR data

Introduction | Examples | Session Information | References

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2024-11-15
Started: 2024-06-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
BPV data	BPV
CA data	CA
CNV 5-plex data	CNV5plex
CNV 6-plex data	CNV6plex
concentration calculation function	conc_cal
HIV data	HIV
HR data	HR
LR data	LR
MM data	MM
Main function for clustering	polytect_clust
Function for merging	polytect_merge
Plotting function for clustering results	polytect_plot
Summary function	polytect_summary
Plotting function for silhouette coefficients	sil_plot