highthroughputassays
This is the released version of highthroughputassays; for the devel version, see highthroughputassays.
Using Bioconductor with High Throughput Assays
Bioconductor version: Release (3.23)
The workflow illustrates use of the flow cytometry packages to load, transform and visualize the flow data and gate certain populations in the dataset. The workflow loads the `flowCore`, `flowStats` and `flowWorkspace` packages and its dependencies. It loads the ITN data with 15 samples, each of which includes, in addition to FSC and SSC, 5 fluorescence channels: CD3, CD4, CD8, CD69 and HLADR.
Author: Bioconductor Package Maintainer [aut, cre]
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
citation("highthroughputassays")):
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")
BiocManager::install("highthroughputassays")
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("highthroughputassays")| Using Bioconductor with High Throughput Assays | HTML | R Script |
Details
| biocViews | ImmunoOncologyWorkflow, ProteomicsWorkflow, Workflow |
| Version | 1.36.0 |
| License | Artistic-2.0 |
| Depends | R (>= 3.3.0), flowCore, flowStats, flowWorkspace |
| Imports | |
| System Requirements | |
| URL | https://www.bioconductor.org/help/workflows/highthroughputassays/ |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | highthroughputassays_1.36.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/highthroughputassays |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/highthroughputassays |
| Package Short Url | https://bioconductor.org/packages/highthroughputassays/ |
| Package Downloads Report | Download Stats |