SiftCell: A robust framework to detect and isolate cell-containing droplets from single-cell RNA sequence reads

. Author manuscript; available in PMC: 2024 Jul 19.

Published in final edited form as: Cell Syst. 2023 Jul 19;14(7):620–628.e3. doi: 10.1016/j.cels.2023.06.002

KEY RESOURCE TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Data
PBMC	10X Genomics	https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_10k_v3
Brain nuclei	10X Genomics	https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/nuclei_900
Colon cell line mixture	Park et al., 2020	GSE149224
Software and algorithms
SiftCell	This paper	https://github.com/jyxi7676/SiftCell/ https://doi.org/10.5281/zenodo.7738864
DropletUtils(version 1.18.0)	Lun et al., 2019	https://doi.org/10.18129/B9.bioc.DropletUtils.
DIEM (version 2.2.0)	Alvarez et al., 2020	https://github.com/marcalva/diem
CellBender (version 0.1.0)	Fleming et al., 2019	https://github.com/broadinstitute/CellBender
Celda (version 1.4.7)	Yang et al., 2020	https://bioconductor.org/packages/release/bioc/html/celda.html
Seurat (version 4.0.2)	Hao et al.. 2021	https://doi.org/10.1016/j.cell.2021.04.048