Other packages > Find by keyword >

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", "2.0.1")



Attach the package and use:
library("dsb")
Maintained by
Matthew Mulè
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-02-08
Latest Update: 2025-04-02
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 2.0.1, https://cran.r-project.org/web/packages/dsb. Accessed 27 Aug. 2026.
Previous versions and publish date:
(2026-07-09 07:33), 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), 2.0.0 (2025-04-02 22:30)
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

IntervalQuestionStat  
Tools to Deal with Interval-Valued Responses in Questionnaires
A user-friendly toolbox for doing the statistical analysis of interval-valued responses in question ...
Download / Learn more Package Citations See dependency  
ROI.plugin.qpoases  
'qpOASES' Plugin for the 'R' Optimization Infrastructure
Enhances the 'R' Optimization Infrastructure ('ROI') package with the quadratic solver 'qpOASES'. M ...
Download / Learn more Package Citations See dependency  
Bodi  
Boosting Diversity in Regression Ensembles
A gradient boosting-based algorithm by incorporating a diversity term to guide the gradient boosting ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
BetterReg  
Better Statistics for OLS and Binomial Logistic Regression
Provides squared semi partial correlations, tolerance, Mahalanobis, Likelihood Ratio Chi Square, and ...
Download / Learn more Package Citations See dependency  
robustX  
'eXtra' / 'eXperimental' Functionality for Robust Statistics
Robustness -- 'eXperimental', 'eXtraneous', or 'eXtraordinary' Functionality for Robust Statistics. ...
Download / Learn more Package Citations See dependency  

28,332

R Packages

239,283

Dependencies

75,113

Author Associations

28,333

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA