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
Author: H. Robert Frost [aut], Azka Javaid [aut, cre]
Maintainer: Azka Javaid < at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
CRAN checks: STREAK results


Reference manual: STREAK.pdf
Vignettes: STREAKvignette


Package source: STREAK_1.0.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
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_0.1.0.tgz
Old sources: STREAK archive


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