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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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scds")
Introduction to the scds package HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

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
See More
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 scds_1.19.0.tar.gz
Windows Binary scds_1.19.0.zip
macOS Binary (x86_64) scds_1.19.0.tgz
macOS Binary (arm64) scds_1.19.0.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