simpleSingleCell

DOI: 10.18129/B9.bioc.simpleSingleCell    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see simpleSingleCell.

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

Bioconductor version: 3.9

This workflow implements a low-level analysis pipeline for scRNA-seq data using scran, scater and other Bioconductor packages. It describes how to perform quality control on the libraries, normalization of cell-specific biases, basic data exploration, cell cycle phase identification, doublet detection and batch correction. Procedures to detect highly variable genes, significantly correlated genes and subpopulation-specific marker genes are also shown. These analyses are demonstrated on publicly available scRNA-seq data sets from a variety of protocols including SMART-seq2 and 10X Genomics.

Author: Aaron Lun [aut, cre], Davis McCarthy [aut], John Marioni [aut]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	01. Introduction
HTML	R Script	02. Read count data
HTML	R Script	03. UMI count data
HTML	R Script	04. Droplet-based data
HTML	R Script	05. Correcting batch effects
HTML	R Script	06. Quality control details
HTML	R Script	07. Spike-in normalization
HTML	R Script	08. Detecting doublets
HTML	R Script	09. Advanced variance modelling
HTML	R Script	10. Detecting differential expression
HTML	R Script	11. Scalability for big data
HTML	R Script	12. Further analysis strategies

Details

biocViews	ImmunoOncologyWorkflow, SingleCellWorkflow, Workflow
Version	1.8.0
License	Artistic-2.0
Depends
Imports	BiocStyle, callr, rmarkdown
LinkingTo
Suggests	knitr, readxl, R.utils, Matrix, SingleCellExperiment, scater, scran, DropletUtils, org.Hs.eg.db, org.Mm.eg.db, EnsDb.Hsapiens.v86, TxDb.Mmusculus.UCSC.mm10.ensGene, dynamicTreeCut, cluster, igraph, Rtsne, pheatmap, limma, edgeR, BiocParallel, BiocFileCache, BiocNeighbors, BiocSingular, batchelor, scRNAseq, TENxBrainData
SystemRequirements
Enhances
URL	https://www.bioconductor.org/help/workflows/simpleSingleCell/
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_1.8.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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