scry

DOI: 10.18129/B9.bioc.scry  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scry.

Small-Count Analysis Methods for High-Dimensional Data

Bioconductor version: 3.16

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.

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

Maintainer: Kelly Street <street.kelly at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scry")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scry")

 

HTML	R Script	Overview of Scry Methods
HTML	R Script	Scry Methods For Larger Datasets
PDF		Reference Manual

Details

biocViews	DimensionReduction, GeneExpression, Normalization, PrincipalComponent, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.10.0
In Bioconductor since	BioC 3.11 (R-4.0) (3 years)
License	Artistic-2.0
Depends	R (>= 4.0), stats, methods
Imports	DelayedArray, glmpca (>= 0.2.0), HDF5Array, Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular
LinkingTo
Suggests	markdown, BiocGenerics, covr, DuoClustering2018, ggplot2, knitr, rmarkdown, TENxPBMCData, testthat
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/scry.html
BugReports	https://github.com/kstreet13/scry/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	scry_1.10.0.tar.gz
Windows Binary	scry_1.10.0.zip
macOS Binary (x86_64)	scry_1.10.0.tgz
macOS Binary (arm64)	scry_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scry
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scry
Bioc Package Browser	https://code.bioconductor.org/browse/scry/
Package Short Url	https://bioconductor.org/packages/scry/
Package Downloads Report	Download Stats