STREAK-package: STREAK: Receptor Abundance Estimation using Feature Selection...

In STREAK: Receptor Abundance Estimation using Feature Selection and Gene Set Scoring

STREAK: Receptor Abundance Estimation using Feature Selection and Gene Set Scoring

Description

Performs receptor abundance estimation for single cell RNA-sequencing data using a supervised feature selection mechanism and a thresholded gene set scoring procedure. 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 reduced rank reconstruction and rank-k selection is detailed in: Javaid et al., (2022) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/2022.10.08.511197")}. Gene set scoring procedure is described in: Frost et al., (2020) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/nar/gkaa582")}. 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]

STREAK documentation built on Nov. 18, 2023, 1:11 a.m.