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dsb  

Normalize & Denoise Droplet Single Cell Protein Data (CITE-Seq)
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", "2.0.0")



Attach the package and use:
library("dsb")
Maintained by
Matthew Mulè
[Scholar Profile | Author Map]
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 2.0.0, https://cran.r-project.org/web/packages/dsb. Accessed 07 May. 2025.
Previous versions and publish date:
0.1.0 (2021-02-08 10:20), 0.2.0 (2021-09-03 02:20), 0.3.0 (2022-01-05 10:50), 1.0.0 (2022-03-14 09:10), 1.0.1 (2022-03-14 19:10), 1.0.2 (2022-05-27 10:40), 1.0.3 (2023-03-18 00:20), 1.0.4 (2024-06-16 04:10)
Other packages that cited dsb R package
View dsb citation profile
Other R packages that dsb depends, imports, suggests or enhances
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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