scry
This is the development version of scry; for the stable release version, see scry.
Small-Count Analysis Methods for High-Dimensional Data
Bioconductor version: Development (3.24)
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>
citation("scry")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| Overview of Scry Methods | HTML | R Script |
| Scry Methods For Larger Datasets | HTML | R Script |
| Reference Manual |
Details
| biocViews | DimensionReduction, GeneExpression, Normalization, PrincipalComponent, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0), stats, methods |
| Imports | DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular |
| System Requirements | |
| URL | https://bioconductor.org/packages/scry.html |
| Bug Reports | https://github.com/kstreet13/scry/issues |
See More
| Suggests | BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | BatchSVG |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scry_1.25.0.tar.gz |
| Windows Binary (x86_64) | scry_1.25.0.zip |
| macOS Binary (big-sur-x86_64) | scry_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | scry_1.25.0.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 |