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dsb
View on CRAN: Click
here
Download and install dsb package within the R console
Install from CRAN:
install.packages("dsb")
Install from Github:
library("remotes")
install_github("cran/dsb")
Install by package version:
library("remotes")
install_version("dsb", "1.0.4")
Attach the package and use:
library("dsb")
Maintained by
Matthew Mulè
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
10.32614/CRAN.package.dsb . https://github.com/niaid/dsb/issues . https://github.com/niaid/dsb . dsb citation info . dsb results . dsb.pdf . End-to-end CITE-seq analysis workflow using dsb for ADT normalization and Seurat for multimodal clustering . Normalizing ADTs for datasets without empty droplets with the dsb function ModelNegativeADTnorm . Understanding how the dsb method works . dsb_1.0.4.tar.gz . dsb_1.0.4.zip . dsb_1.0.4.zip . dsb_1.0.4.zip . dsb_1.0.4.tgz . dsb_1.0.4.tgz . dsb_1.0.4.tgz . dsb_1.0.4.tgz . dsb_1.0.4.tgz . dsb_1.0.4.tgz . dsb archive . https://CRAN.R-project.org/package=dsb .
First Published: 2021-02-08
Latest Update: 2023-03-17
Description:
This lightweight R package provides a method for normalizing and denoising protein expression data from droplet based single cell experiments. Raw protein Unique Molecular Index (UMI) counts from sequencing DNA-conjugated antibody derived tags (ADT) in droplets (e.g. 'CITE-seq') have substantial measurement noise. Our experiments and computational modeling revealed two major components of this noise: 1) protein-specific noise originating from ambient, unbound antibody encapsulated in droplets that can be accurately inferred via the expected protein counts detected in empty droplets, and 2) droplet/cell-specific noise revealed via the shared variance component associated with isotype antibody controls and background protein counts in each cell. This package normalizes and removes both of these sources of noise from raw protein data derived from methods such as 'CITE-seq', 'REAP-seq', 'ASAP-seq', 'TEA-seq', 'proteogenomic' data from the Mission Bio platform, etc. See the vignette for tutorials on how to integrate dsb with 'Seurat' and 'Bioconductor' and how to use dsb in 'Python'. Please see our paper Mul
How to cite:
Matthew Mulè (2021). dsb: Normalize & Denoise Droplet Single Cell Protein Data (CITE-Seq). R package version 1.0.4, https://cran.r-project.org/web/packages/dsb. Accessed 29 Mar. 2025.
Previous versions and publish date:
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Complete documentation for dsb
Functions, R codes and Examples using
the dsb R package
Some associated functions: DSBNormalizeProtein . ModelNegativeADTnorm . cells_citeseq_mtx . empty_drop_citeseq_mtx . pipe .
Some associated R codes: empty_drop_citeseq_mtx.R . utils-pipe.R . Full dsb package functions and examples
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