scds

DOI: 10.18129/B9.bioc.scds  

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

Bioconductor version: Release (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("scds")

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("scds")

 

HTML	R Script	Introduction to the scds package
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, GeneExpression, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.16.0
In Bioconductor since	BioC 3.9 (R-3.6) (4.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6.0)
Imports	Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC
LinkingTo
Suggests	BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	singleCellTK
Suggests Me	ExperimentSubset, muscData
Links To Me
Build Report

Package Archives

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

Source Package	scds_1.16.0.tar.gz
Windows Binary	scds_1.16.0.zip
macOS Binary (x86_64)	scds_1.16.0.tgz
macOS Binary (arm64)	scds_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scds
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scds
Bioc Package Browser	https://code.bioconductor.org/browse/scds/
Package Short Url	https://bioconductor.org/packages/scds/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive