weitrix

DOI: 10.18129/B9.bioc.weitrix    

This is the development version of weitrix; for the stable release version, see weitrix.

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

Bioconductor version: Development (3.12)

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 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>

Citation (from within R, enter citation("weitrix")):

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.2
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
License LGPL-2.1 | file LICENSE
Depends R (>= 3.6), SummarizedExperiment
Imports methods, utils, stats, assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, dplyr, purrr, ggplot2, rlang, 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_1.1.2.tar.gz
Windows Binary weitrix_1.1.2.zip
macOS 10.13 (High Sierra) weitrix_1.1.2.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

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