Polytect
This is the development version of Polytect; for the stable release version, see Polytect.
An R package for digital data clustering
Bioconductor version: Development (3.24)
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.
Maintainer: Yao Chen <emmachentar at live.com>
citation("Polytect")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("Polytect")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Polytect")| Polytect Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, MultiChannel, Software, ddPCR |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0) |
| Imports | stats, utils, grDevices, mvtnorm, sn, dplyr, flowPeaks, ggplot2, tidyverse, cowplot, mlrMBO, DiceKriging, smoof, ParamHelpers, lhs, rgenoud, BiocManager |
| System Requirements | |
| URL | https://github.com/emmachenlingo/Polytect |
| Bug Reports | https://github.com/emmachenlingo/Polytect/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown, ddPCRclust |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Polytect_1.5.0.tar.gz |
| Windows Binary (x86_64) | Polytect_1.5.0.zip |
| macOS Binary (big-sur-x86_64) | Polytect_1.5.0.tgz |
| macOS Binary (sonoma-arm64) | Polytect_1.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Polytect |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Polytect |
| Bioc Package Browser | https://code.bioconductor.org/browse/Polytect/ |
| Package Short Url | https://bioconductor.org/packages/Polytect/ |
| Package Downloads Report | Download Stats |