Package: scds 2.1.0

Dennis Kostka

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

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.

Authors:Dennis Kostka [aut, cre], Bais Abha [aut]

scds_2.1.0.tar.gz
scds_2.1.0.zip(r-4.7)scds_2.1.0.zip(r-4.6)scds_2.1.0.zip(r-4.5)
scds_2.1.0.tgz(r-4.6-any)scds_2.1.0.tgz(r-4.5-any)
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scds_2.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scds/json (API)

# Install 'scds' in R:

install.packages('scds', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

sce_chcl - Example single cell experiment ('SingleCellExperiment') object

On BioConductor:scds-2.1.0(bioc 3.24)scds-2.0.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

singlecell rnaseq qualitycontrol preprocessing transcriptomics geneexpression sequencing software classification

6.75 score 1 packages 268 scripts 898 downloads 7 mentions 3 exports 37 dependencies

Last updated from:731410b2fd. Checks:1 FAIL, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	FAIL	1447
linux-devel-x86_64	OK	358
source / vignettes	OK	309
linux-release-x86_64	OK	311
macos-release-arm64	OK	220
macos-oldrel-arm64	OK	218
windows-devel	OK	231
windows-release	OK	208
windows-oldrel	OK	211
wasm-release	OK	164

Exports:bcds cxds cxds_bcds_hybrid

Dependencies:abind Biobase BiocGenerics cli data.table DelayedArray dplyr generics GenomicRanges glue IRanges jsonlite lattice lifecycle magrittr Matrix MatrixGenerics matrixStats pillar pkgconfig pROC R6 Rcpp rlang S4Arrays S4Vectors Seqinfo SingleCellExperiment SparseArray SummarizedExperiment tibble tidyselect utf8 vctrs withr xgboost XVector

scds:single cell doublet scoring: In-silico doublet annotation for single cell RNA sequencing data

Rendered fromscds.Rmdusingknitr::rmarkdown

Last update: 2022-09-30
Started: 2019-03-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Find doublets/multiplets in UMI scRNA-seq data;	bcds
Find doublets/multiplets in UMI scRNA-seq data;	cxds
Find doublets/multiples in UMI scRNA-seq data;	cxds_bcds_hybrid
Extract top-scoring gene pairs from an SingleCellExperiment where cxds has been run	cxds_getTopPairs
Wrapper for getting doublet calls	get_dblCalls_ALL
Derive doublet calls from doublset scores	get_dblCalls_dist
Derive doublet calls from classification probabilities	get_dblCalls_ROC
Example single cell experiment ('SingleCellExperiment') object	sce_chcl