Package: scds 1.23.0

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]

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scds.pdf |scds.html✨
scds/json (API)
NEWS

# 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-1.23.0(bioc 3.21)scds-1.22.0(bioc 3.20)

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

6.46 score 1 packages 136 scripts 930 downloads 7 mentions 3 exports 49 dependencies

Last updated 23 days agofrom:f0cf1fa30e. Checks:OK: 5 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	OK	Oct 31 2024
R-4.5-linux	OK	Oct 31 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	WARNING	Oct 31 2024

Exports:bcds cxds cxds_bcds_hybrid

Dependencies:abind askpass Biobase BiocGenerics cli crayon curl data.table DelayedArray dplyr fansi generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges jsonlite lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig plyr pROC R6 Rcpp rlang S4Arrays S4Vectors SingleCellExperiment SparseArray SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs withr xgboost XVector zlibbioc

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

Rendered fromscds.Rmdusingknitr::rmarkdownon Oct 31 2024.

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