OSCA.workflows
This is the released version of OSCA.workflows; for the devel version, see OSCA.workflows.
OSCA Workflows
Bioconductor version: Release (3.23)
Deploys the workflows of the "Orchestrating Single Cell Analysis with Bioconductor" book. This contains worked case studies of analyses of a variety of single-cell datasets, each proceeding from a SingleCellExperiment object. Exposition is generally minimal other than for dataset-specific justifications for parameter tweaks; refer to the other books in the OCSA collection for a detailed explanation of the theoretical basis of each step. It is intended for readers who already know the background and just want some code to copy and paste into their own 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.workflows")):Robert Amezquita, Aaron Lun, Stephanie Hicks, Raphael Gottardo. OSCA.workflows: OSCA Workflows. doi:10.18129/B9.bioc.OSCA.workflows, R package version 1.20.0, https://bioconductor.org/packages/OSCA.workflows.
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.workflows")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 4.0 |
| Depends | AnnotationHub, batchelor, BiocFileCache, BiocNeighbors, BiocParallel, BiocSingular, bluster, celldex, cluster, DropletTestFiles, DropletUtils, dynamicTreeCut, edgeR, EnsDb.Hsapiens.v86, gridExtra, HCAData, igraph, limma, org.Hs.eg.db, org.Mm.eg.db, pheatmap, rebook, rmarkdown, scater, scPCA, scran, scRNAseq, scuttle, SingleR, viridis |
| Imports | |
| System Requirements | |
| URL | https://github.com/OSCA-source/OSCA.workflows |
See More
| Suggests | BiocManager, rmarkdown, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSCA.advanced, OSCA.basic, OSCA.multisample |
| Suggests Me | OSCA, rebook |
| 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.workflows |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/OSCA.workflows |
| Package Short Url | https://bioconductor.org/packages/OSCA.workflows/ |
| Package Downloads Report | Download Stats |