simpleSingleCell
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Bioconductor version: Release (3.20)
Once a proud workflow package, this is now a shell of its former self. Almost all of its content has been cannibalized for use in the "Orchestrating Single-Cell Analyses with Bioconductor" book at https://osca.bioconductor.org. Most vignettes here are retained as reminders of the glory that once was, also providing redirection for existing external links to the relevant OSCA book chapters.
Author: Aaron Lun [aut, cre], Davis McCarthy [aut], John Marioni [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("simpleSingleCell")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("simpleSingleCell")
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("simpleSingleCell")| 01. Introduction | HTML | |
| 02. Read count data | HTML | |
| 03. UMI count data | HTML | |
| 04. Droplet-based data | HTML | |
| 05. Correcting batch effects | HTML | |
| 06. Quality control details | HTML | |
| 07. Spike-in normalization | HTML | |
| 08. Detecting doublets | HTML | |
| 09. Advanced variance modelling | HTML | |
| 10. Detecting differential expression | HTML | |
| 11. Advanced batch correction | HTML | |
| 12. Scalability for big data | HTML | |
| 13. Further analysis strategies | HTML | R Script |
Details
| biocViews | ImmunoOncologyWorkflow, SingleCellWorkflow, Workflow |
| Version | 1.30.0 |
| License | Artistic-2.0 |
| Depends | |
| Imports | utils, methods, knitr, callr, rmarkdown, CodeDepends, BiocStyle |
| System Requirements | |
| URL | https://www.bioconductor.org/help/workflows/simpleSingleCell/ |
See More
| Suggests | readxl, R.utils, SingleCellExperiment, scater, scran, limma, BiocFileCache, org.Mm.eg.db |
| 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 | simpleSingleCell_1.30.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/simpleSingleCell |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/simpleSingleCell |
| Package Short Url | https://bioconductor.org/packages/simpleSingleCell/ |
| Package Downloads Report | Download Stats |