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

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) <doi:10.1016/j.cell.2021.04.048>, Stuart et al., (2019) <doi:10.1016/j.cell.2019.05.031>, Butler et al., (2018) <doi:10.1038/nbt.4096> and Satija et al., (2015) <doi:10.1038/nbt.3192>. Method for reduced rank reconstruction and rank-k selection is detailed in: Javaid et al., (2022) <doi:10.1101/2022.10.08.511197>. Gene set scoring procedure is described in: Frost et al., (2020) <doi:10.1093/nar/gkaa582>. Clustering method is outlined in: Song et al., (2020) <doi:10.1093/bioinformatics/btaa613> and Wang et al., (2011) <doi:10.32614/RJ-2011-015>.

Version:	1.0.0
Depends:	R (≥ 2.10)
Imports:	Ckmeans.1d.dp, Matrix, Seurat, SPECK, stats, VAM
Suggests:	knitr, rmarkdown
Published:	2023-11-17
DOI:	10.32614/CRAN.package.STREAK
Author:	H. Robert Frost [aut], Azka Javaid [aut, cre]
Maintainer:	Azka Javaid <azka.javaid.gr at dartmouth.edu>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation:	no
CRAN checks:	STREAK results

Documentation:

Reference manual:	STREAK.pdf
Vignettes:	STREAKvignette

Downloads:

Package source:	STREAK_1.0.0.tar.gz
Windows binaries:	r-devel: STREAK_1.0.0.zip, r-release: STREAK_1.0.0.zip, r-oldrel: STREAK_1.0.0.zip
macOS binaries:	r-release (arm64): STREAK_1.0.0.tgz, r-oldrel (arm64): STREAK_1.0.0.tgz, r-release (x86_64): STREAK_1.0.0.tgz, r-oldrel (x86_64): STREAK_1.0.0.tgz
Old sources:	STREAK archive

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