Package: scry 1.25.0

Kelly Street

scry: Small-Count Analysis Methods for High-Dimensional Data

Many modern biological datasets consist of small counts that are not well fit by standard linear-Gaussian methods such as principal component analysis. This package provides implementations of count-based feature selection and dimension reduction algorithms. These methods can be used to facilitate unsupervised analysis of any high-dimensional data such as single-cell RNA-seq.

Authors:Kelly Street [aut, cre], F. William Townes [aut, cph], Davide Risso [aut], Stephanie Hicks [aut]

scry_1.25.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
scry/json (API)

# Install 'scry' in R:

install.packages('scry', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kstreet13/scry/issues

On BioConductor:scry-1.25.0(bioc 3.24)scry-1.24.0(bioc 3.23)

dimensionreduction geneexpression normalization principalcomponent rnaseq software sequencing singlecell transcriptomics

8.07 score 23 stars 1 packages 171 scripts 742 downloads 1 mentions 3 exports 36 dependencies

Last updated from:abf8f7fa96. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	242
linux-devel-x86_64	NOTE	491
source / vignettes	OK	431
linux-release-x86_64	NOTE	323
macos-release-arm64	NOTE	224
macos-oldrel-arm64	NOTE	167
windows-devel	NOTE	1202
windows-release	NOTE	1001
windows-oldrel	NOTE	955
wasm-release	OK	191

Exports:devianceFeatureSelection GLMPCA nullResiduals

Dependencies:abind assorthead beachmat BH Biobase BiocGenerics BiocParallel BiocSingular codetools cpp11 DelayedArray formatR futile.logger futile.options generics GenomicRanges glmpca IRanges irlba lambda.r lattice MASS Matrix MatrixGenerics matrixStats Rcpp rsvd S4Arrays S4Vectors ScaledMatrix Seqinfo SingleCellExperiment snow SparseArray SummarizedExperiment XVector

Overview of Scry Methods

Will Townes

Rendered fromscry.Rmdusingknitr::knitron May 30 2026.

Last update: 2020-10-13
Started: 2020-04-21

Scry Methods For Larger Datasets

Will Townes

Rendered frombigdata.Rmdusingknitr::knitron May 30 2026.

Last update: 2020-10-13
Started: 2020-08-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Feature selection by approximate multinomial deviance	devianceFeatureSelection devianceFeatureSelection,DelayedArray-method devianceFeatureSelection,Matrix-method devianceFeatureSelection,matrix-method devianceFeatureSelection,SummarizedExperiment-method
Generalized principal components analysis for non-normally distributed data	GLMPCA GLMPCA,Matrix-method GLMPCA,matrix-method GLMPCA,SummarizedExperiment-method
Residuals from an approximate multinomial null model	nullResiduals nullResiduals,ANY-method nullResiduals,Matrix-method nullResiduals,matrix-method nullResiduals,SingleCellExperiment-method nullResiduals,SummarizedExperiment-method