weitrix

DOI: 10.18129/B9.bioc.weitrix    

Tools for matrices with precision weights, test and explore weighted or sparse data

Bioconductor version: Release (3.15)

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 to account for known predictors of precision. Find rows with excess variability. Perform differential testing and find rows with the largest confident differences. 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 "4.2") and enter:

if (!require("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
HTML	R Script	5. Proportions data example with SLAM-Seq
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataRepresentation, DimensionReduction, GeneExpression, RNASeq, Regression, SingleCell, Software, Transcriptomics
Version	1.8.0
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	LGPL-2.1 | file LICENSE
Depends	R (>= 3.6), SummarizedExperiment
Imports	methods, utils, stats, grDevices, assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, topconfects, dplyr, purrr, ggplot2, rlang, scales, reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	weitrix_1.8.0.tar.gz
Windows Binary	weitrix_1.8.0.zip
macOS Binary (x86_64)	weitrix_1.8.0.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