weitrix

DOI: 10.18129/B9.bioc.weitrix    

Weighted matrix manipulation, finding components of variation with weighted or sparse data

Bioconductor version: Release (3.11)

Data type and tools for working with matrices having precision weights and missing data. This package provides a common representation and tools that can be used with many types of high-throughput data. The meaning of the weights is compatible with usage in the base R function "lm" and the package "limma". Calibrate weights by scaling weights row-wise to account for known predictors of precision. Find PCA-like components of variation even with many missing values, rotated so that individual components may be meaningfully interpreted. DelayedArray matrices and BiocParallel are supported.

Author: Paul Harrison [aut, cre]

Maintainer: Paul Harrison <paul.harrison at monash.edu>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("weitrix")

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("weitrix")

 

HTML		1. Concepts and practical details
HTML	R Script	2. poly(A) tail length example
HTML	R Script	3. Alternative polyadenylation
HTML	R Script	4. RNA-Seq expression example
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataRepresentation, DimensionReduction, GeneExpression, RNASeq, Regression, SingleCell, Software, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.11 (R-4.0) (0.5 years)
License	LGPL-2.1 | file LICENSE
Depends	R (>= 4.0), SummarizedExperiment
Imports	methods, utils, stats, assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, dplyr, purrr, ggplot2, scales, reshape2, RhpcBLASctl
LinkingTo
Suggests	knitr, rmarkdown, tidyverse, airway, edgeR, topconfects, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL
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	weitrix_1.0.0.tar.gz
Windows Binary	weitrix_1.0.0.zip
macOS 10.13 (High Sierra)	weitrix_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/weitrix
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/weitrix
Package Short Url	https://bioconductor.org/packages/weitrix/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive