scds

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see scds.

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


Bioconductor version: 3.10

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 "3.6") 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

Details

biocViews Classification, GeneExpression, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.2.0
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
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Suggests BiocStyle, knitr, rsvd, Rtsne, scater, cowplot
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Package Archives

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

Source Package scds_1.2.0.tar.gz
Windows Binary scds_1.2.0.zip
Mac OS X 10.11 (El Capitan) scds_1.2.0.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 3.10 Source Archive