DelayedMatrixStats
This is the development version of DelayedMatrixStats; for the stable release version, see DelayedMatrixStats.
Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
Bioconductor version: Development (3.24)
A port of the 'matrixStats' API for use with DelayedMatrix objects from the 'DelayedArray' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.
Author: Peter Hickey [aut, cre]
, Hervé Pagès [ctb], Aaron Lun [ctb]
Maintainer: Peter Hickey <peter.hickey at gmail.com>
citation("DelayedMatrixStats")):
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("DelayedMatrixStats")
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("DelayedMatrixStats")| Overview of DelayedMatrixStats | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataRepresentation, Infrastructure, Software |
| Version | 1.35.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 years) |
| License | MIT + file LICENSE |
| Depends | MatrixGenerics(>= 1.15.1), DelayedArray(>= 0.31.7) |
| Imports | methods, sparseMatrixStats(>= 1.13.2), Matrix (>= 1.5-0), S4Vectors(>= 0.17.5), IRanges(>= 2.25.10), SparseArray(>= 1.5.19) |
| System Requirements | |
| URL | https://github.com/PeteHaitch/DelayedMatrixStats |
| Bug Reports | https://github.com/PeteHaitch/DelayedMatrixStats/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, microbenchmark, profmem, HDF5Array, matrixStats (>= 1.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | AUCell, batchelor, biscuiteer, bsseq, Cepo, DeconvoBuddies, dmrseq, dreamlet, DropletUtils, FRASER, glmGamPoi, GSVA, lemur, methrix, methylSig, mia, minfi, mumosa, NetActivity, PCAtools, RBedMethyl, recountmethylation, SCArray, scFeatures, scMerge, scone, Seqtometry, singleCellTK, sparrow, SpliceWiz, SVP, weitrix, celldex, spatialGE |
| Suggests Me | blase, condiments, dandelionR, DelayedArray, escape, EWCE, HDF5Array, MatrixGenerics, mbkmeans, ScaledMatrix, scater, scPCA, scran, scuttle, slingshot, SplineDV, tradeSeq, TrajectoryUtils, Voyager, ClustAssess |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DelayedMatrixStats_1.35.0.tar.gz |
| Windows Binary (x86_64) | DelayedMatrixStats_1.35.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | DelayedMatrixStats_1.35.0.tgz |
| macOS Binary (sonoma-arm64) | DelayedMatrixStats_1.35.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DelayedMatrixStats |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DelayedMatrixStats |
| Bioc Package Browser | https://code.bioconductor.org/browse/DelayedMatrixStats/ |
| Package Short Url | https://bioconductor.org/packages/DelayedMatrixStats/ |
| Package Downloads Report | Download Stats |