weitrix
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see weitrix.
Weighted matrix manipulation, finding components of variation with weighted or sparse data
Bioconductor version: 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>
citation("weitrix")):
Installation
To install this package, start R (version "4.0") 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")| 1. Concepts and practical details | HTML | |
| 2. poly(A) tail length example | HTML | R Script |
| 3. Alternative polyadenylation | HTML | R Script |
| 4. RNA-Seq expression example | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataRepresentation, DimensionReduction, GeneExpression, RNASeq, Regression, SingleCell, Software, Transcriptomics |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, tidyverse, airway, edgeR, topconfects, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, testthat (>= 2.1.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/weitrix/ |
| Package Short Url | https://bioconductor.org/packages/weitrix/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |