scds

This is the development version of scds; for the stable release version, see scds.

In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data

Bioconductor version: Development (3.19)

In single cell RNA sequencing (scRNA-seq) data combinations of cells are sometimes considered a single cell (doublets). The scds package provides methods to annotate doublets in scRNA-seq data computationally.

Author: Dennis Kostka [aut, cre], Bais Abha [aut]

Maintainer: Dennis Kostka <kostka at pitt.edu>

Citation (from within R, enter citation("scds")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("scds")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, GeneExpression, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.19.0
In Bioconductor since	BioC 3.9 (R-3.6) (5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6.0)
Imports	Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC
System Requirements
URL

Suggests	BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me	singleCellTK
Suggests Me	ExperimentSubset, muscData
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/scds
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scds
Package Short Url	https://bioconductor.org/packages/scds/
Package Downloads Report	Download Stats