growkar
This is the development version of growkar; to use it, please install the devel version of Bioconductor.
SummarizedExperiment Infrastructure for Microbial Growth Phenotyping
Bioconductor version: Development (3.24)
growkar provides Bioconductor-native infrastructure for high-throughput microbial growth phenotyping from plate-based assays such as optical density (OD) measurements. The package is built around SummarizedExperiment as its canonical data model, with OD measurements in assays, timepoint annotations in rowData, sample annotations in colData, and derived phenotypes in metadata. growkar supports data import, quality control, normalization, empirical growth-rate estimation, exponential-phase detection, and parametric modeling of growth dynamics. These workflows enable extraction of biologically meaningful phenotypes including lag time, growth rate, doubling time, and carrying capacity, and allow growth-derived phenotypes to be integrated with other Bioconductor analyses in microbial systems biology and multi-omics studies. The data-structure and analysis layers depend only on core Bioconductor infrastructure; graphing is optional and provided by 'plot_*' functions that are enabled when suggested graphics packages are installed.
Author: Pooja Sethiya [aut, cre]
Maintainer: Pooja Sethiya <poojasethiya24 at gmail.com>
citation("growkar")):
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("growkar")
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("growkar")| growkar-introduction | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, ExperimentalDesign, Infrastructure, Normalization, QualityControl, Software, SystemsBiology, Visualization |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | methods, S4Vectors, SummarizedExperiment, tidySummarizedExperiment, dplyr, purrr, rlang, stats, tibble, tidyr, utils |
| System Requirements | |
| URL | https://github.com/sethiyap/growkar |
| Bug Reports | https://github.com/sethiyap/growkar/issues |
See More
| Suggests | ggplot2, RColorBrewer, knitr, remotes, rmarkdown, testthat (>= 3.0.0) |
| 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 | growkar_0.99.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | growkar_0.99.2.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/growkar |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/growkar |
| Bioc Package Browser | https://code.bioconductor.org/browse/growkar/ |
| Package Short Url | https://bioconductor.org/packages/growkar/ |
| Package Downloads Report | Download Stats |