scds

DOI: 10.18129/B9.bioc.scds    

This is the development version of scds; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (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 (!requireNamespace("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")

 

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 1.1.2
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
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
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package scds_1.1.2.tar.gz
Windows Binary scds_1.1.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scds_1.1.2.tgz
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 http://bioconductor.org/packages/scds/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: