OSCA.basic
This is the released version of OSCA.basic; for the devel version, see OSCA.basic.
Single-Cell Analysis Basics
Bioconductor version: Release (3.23)
Deploys basic analysis chapters for the "Orchestrating Single Cell Analysis with Bioconductor" book. This describes the steps of a simple single-cell RNA-seq analysis, involving quality control, normalization, various forms of dimensionality reduction, clustering into subpopulations, detection of marker genes, and annotation of cell types. It is intended for users who already have some familiarity with R and want to get hands-on with some basic single-cell analyses.
Author: Robert Amezquita [aut], Aaron Lun [aut], Stephanie Hicks [aut], Raphael Gottardo [aut], Peter Hickey [cre]
Maintainer: Peter Hickey <peter.hickey at gmail.com>
citation("OSCA.basic")):Robert Amezquita, Aaron Lun, Stephanie Hicks, Raphael Gottardo. OSCA.basic: Single-Cell Analysis Basics. doi:10.18129/B9.bioc.OSCA.basic, R package version 1.20.0, https://bioconductor.org/packages/OSCA.basic.
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.basic")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("OSCA.basic")| Link to book | HTML |
| 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 4.0 |
| Depends | AnnotationHub, apcluster, AUCell, BiocFileCache, BiocSingular, bluster, celldex, cluster, dendextend, dynamicTreeCut, GO.db, gridExtra, GSEABase, igraph, limma, mbkmeans, org.Mm.eg.db, pheatmap, rebook, rmarkdown, RMTstat, robustbase, Rtsne, scater, scran, scrapper, scRNAseq, scuttle, SingleR, statmod, viridis |
| Imports | OSCA.workflows |
| System Requirements | |
| URL | https://github.com/OSCA-source/OSCA.basic |
See More
| Suggests | rmarkdown, knitr, OSCA.advanced |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSCA.advanced |
| Suggests Me | OSCA, OSCA.multisample |
| 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.basic |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/OSCA.basic |
| Package Short Url | https://bioconductor.org/packages/OSCA.basic/ |
| Package Downloads Report | Download Stats |