scds
This package is for version 3.18 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: 3.18
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("scds")):
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")| Introduction to the scds package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, GeneExpression, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.18.0 |
| 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_1.18.0.tar.gz |
| Windows Binary | scds_1.18.0.zip |
| macOS Binary (x86_64) | scds_1.18.0.tgz |
| macOS Binary (arm64) | scds_1.18.0.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 |