background noise removal using CellBender

epigen / scrnaseq_processing_seurat

A Snakemake workflow for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.

MIT License

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background noise removal using CellBender #8

Open sreichl opened 1 year ago

sreichl commented 1 year ago

review why important: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02978-x
published in Nature Methods: https://www.nature.com/articles/s41592-023-01943-7
e.g., CellBender https://cellbender.readthedocs.io/en/latest/

sreichl commented 6 months ago

alternative SoupX

https://cran.r-project.org/web/packages/SoupX/vignettes/pbmcTutorial.html
https://github.com/constantAmateur/SoupX