OSCA.advanced
This is the released version of OSCA.advanced; for the devel version, see OSCA.advanced.
Advanced Single-Cell Analysis
Bioconductor version: Release (3.23)
Deploys the advanced analysis chapters for the "Orchestrating Single Cell Analysis with Bioconductor" book. This describes the more complex steps of a single-cell RNA-seq analysis ranging from doublet detection, cell cycle assignment, specific steps for processing droplet data, nuclei-specific analyses, trajectory analyses, integrated analyses with protein abundances, and interactive visualization. It also elaborates on some of the basic analysis steps, focusing on alternative strategies and theoretical considerations. 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], Ludwig Geistlinger [cre], Peter Hickey [ctb]
Maintainer: Ludwig Geistlinger <ludwig_geistlinger at hms.harvard.edu>
citation("OSCA.advanced")):Robert Amezquita, Aaron Lun, Stephanie Hicks, Raphael Gottardo. OSCA.advanced: Advanced Single-Cell Analysis. doi:10.18129/B9.bioc.OSCA.advanced, R package version 1.20.1, https://bioconductor.org/packages/OSCA.advanced.
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.advanced")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 | 1.20.1 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | CC BY 4.0 |
| Depends | AnnotationHub, batchelor, BiocFileCache, BiocNeighbors, BiocParallel, BiocSingular, bluster, clustree, corral, densvis, DropletTestFiles, DropletUtils, edgeR, ggbeeswarm, ggplot2, gridExtra, igraph, iSEE, limma, msigdbr, mumosa, org.Mm.eg.db, pheatmap, rebook, rmarkdown, Rtsne, scater, scDblFinder, scPCA, scran, scrapper, scRNAseq (>= 2.17.9), scuttle, SingleR, slingshot, snifter, TENxBrainData, tradeSeq, TSCAN, velociraptor, viridis |
| Imports | OSCA.workflows, OSCA.basic, OSCA.multisample |
| System Requirements | |
| URL | https://github.com/OSCA-source/OSCA.advanced |
See More
| Suggests | rmarkdown, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | OSCA, OSCA.basic |
| 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.advanced |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/OSCA.advanced |
| Package Short Url | https://bioconductor.org/packages/OSCA.advanced/ |
| Package Downloads Report | Download Stats |