scds

This is the released version of scds; for the devel version, see scds.

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

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DOI: 10.18129/B9.bioc.scds

Bioconductor version: Release (3.22)

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 "4.5") 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")

Introduction to the scds package HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, GeneExpression, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics

Version 1.26.0

In Bioconductor since BioC 3.9 (R-3.6) (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 scds_1.26.0.tar.gz

Windows Binary (x86_64) scds_1.25.0.zip (64-bit only)

macOS Binary (x86_64) scds_1.26.0.tgz

macOS Binary (arm64) scds_1.26.0.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