weitrix
This is the development version of weitrix; for the stable release version, see weitrix.
Tools for matrices with precision weights, test and explore weighted or sparse data
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Paul Harrison <paul.harrison at monash.edu>
citation("weitrix")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("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")| 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 |
| 5. Proportions data example with SLAM-Seq | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataRepresentation, DimensionReduction, GeneExpression, RNASeq, Regression, SingleCell, Software, Transcriptomics |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, 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_1.19.0.tar.gz |
| Windows Binary (x86_64) | weitrix_1.19.0.zip |
| macOS Binary (x86_64) | weitrix_1.19.0.tgz |
| macOS Binary (arm64) | weitrix_1.19.0.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 |