kstreet13 / scry

Collection of analysis methods for small count data generated by rafalab members (the methods, not the data).

scry

The released version of scry can be found on Bioconductor at https://bioconductor.org/packages/scry.

A collection of methods for the analysis of small-count data, such as single-cell RNA-seq.

Included methods:

• Deviance for feature selection
• GLM-PCA for dimension reduction
• Null residuals, a transformation that when combined with PCA approximates GLM-PCA

Planned additions for upcoming release:

• Quasi-UMI normalization for single-cell read counts
• Cell type prediction for scRNA-seq

Installation

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("scry")

The Bioconductor release requires the latest version of R. If you prefer to use the older R 3.6, you can install from the unofficial r3 branch as follows:

remotes::install_github("kstreet13/scry@r3")

The r3 branch is not tested as regularly.

Issues and bug reports

Please use https://github.com/kstreet13/scry/issues to submit issues, bug reports, and comments.