SPECK-package: SPECK: Receptor Abundance Estimation using Reduced Rank...

In SPECK: Receptor Abundance Estimation using Reduced Rank Reconstruction and Clustered Thresholding

SPECK: Receptor Abundance Estimation using Reduced Rank Reconstruction and Clustered Thresholding

Description

Surface Protein abundance Estimation using CKmeans-based clustered thresholding ('SPECK') is an unsupervised learning-based method that performs receptor abundance estimation for single cell RNA-sequencing data based on reduced rank reconstruction (RRR) and a clustered thresholding mechanism. Seurat's normalization method is described in: Hao et al., (2021) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.cell.2021.04.048")}, Stuart et al., (2019) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.cell.2019.05.031")}, Butler et al., (2018) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nbt.4096")} and Satija et al., (2015) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nbt.3192")}. Method for the RRR is further detailed in: Erichson et al., (2019) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18637/jss.v089.i11")} and Halko et al., (2009) arXiv:0909.4061. Clustering method is outlined in: Song et al., (2020) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btaa613")} and Wang et al., (2011) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.32614/RJ-2011-015")}.

Author(s)

Maintainer: Azka Javaid [e-mail]

Authors:

• H. Robert Frost [e-mail]

SPECK documentation built on Nov. 18, 2023, 1:12 a.m.