Package: weitrix
Title: Tools for matrices with precision weights, test and explore
        weighted or sparse data
Version: 1.16.0
Authors@R: person("Paul", "Harrison", email = "paul.harrison@monash.edu", role = c("aut", "cre"), comment=c(ORCID="0000-0002-3980-268X"))
Description: 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.
License: LGPL-2.1 | file LICENSE
Encoding: UTF-8
LazyData: true
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
Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR,
        EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi,
        ComplexHeatmap, patchwork, testthat (>= 2.1.0)
RoxygenNote: 7.2.3
VignetteBuilder: knitr
biocViews: Software, DataRepresentation, DimensionReduction,
        GeneExpression, Transcriptomics, RNASeq, SingleCell, Regression
git_url: https://git.bioconductor.org/packages/weitrix
git_branch: RELEASE_3_19
git_last_commit: b1d9a3f
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-02 02:44:43 UTC; biocbuild
Author: Paul Harrison [aut, cre] (<https://orcid.org/0000-0002-3980-268X>)
Maintainer: Paul Harrison <paul.harrison@monash.edu>
Built: R 4.4.0; ; 2024-05-02 13:42:30 UTC; windows
