OSCA.multisample
This is the released version of OSCA.multisample; for the devel version, see OSCA.multisample.
OSCA for Multiple Samples
Bioconductor version: Release (3.23)
Deploys the multi-sample analysis chapters for the "Orchestrating Single Cell Analysis with Bioconductor" book. This describes the handling of multiple samples in a single-cell RNA-seq analysis, starting with integration of multiple datasets into a common space for consistent analyses, differential expression comparisons between conditions based on pseudo-bulk samples, and differential abundance analyses for cell subpopulations. It is intended for readers who are already familiar with basic single-cell analyses, possibly after reading some of the prior books in this collection.
Author: Robert Amezquita [aut], Aaron Lun [aut], Stephanie Hicks [aut], Raphael Gottardo [aut], Alan O'Callaghan [cre]
Maintainer: Alan O'Callaghan <alan.ocallaghan at outlook.com>
citation("OSCA.multisample")):Robert Amezquita, Aaron Lun, Stephanie Hicks, Raphael Gottardo. OSCA.multisample: OSCA for Multiple Samples. doi:10.18129/B9.bioc.OSCA.multisample, R package version 1.20.0, https://bioconductor.org/packages/OSCA.multisample.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("OSCA.multisample")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| No vignettes available | |
| Reference Manual |
Details
| biocViews | ImmunoOncologyWorkflow, SingleCellWorkflow, Software, Workflow |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | CC BY |
| Depends | batchelor, BiocSingular, bluster, DropletUtils, edgeR, gridExtra, igraph, MouseGastrulationData, pheatmap, rebook, rmarkdown, Rtsne, scater, scran, scuttle, SingleR, TENxPBMCData, TSCAN, uwot, viridis |
| Imports | OSCA.workflows |
| System Requirements | |
| URL | https://github.com/OSCA-source/OSCA.multisample |
See More
| Suggests | OSCA.basic, rmarkdown, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSCA.advanced |
| Suggests Me | OSCA |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/OSCA.multisample |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/OSCA.multisample |
| Package Short Url | https://bioconductor.org/packages/OSCA.multisample/ |
| Package Downloads Report | Download Stats |