RNAseqCovarImpute
Impute Covariate Data in RNA Sequencing Studies
Bioconductor version: Release (3.18)
The RNAseqCovarImpute package implements multiple imputation of missing covariates and differential gene expression analysis by: 1) Randomly binning genes into smaller groups, 2) Creating M imputed datasets separately within each bin, where the imputation predictor matrix includes all covariates and the log counts per million (CPM) for the genes within each bin, 3) Estimating gene expression changes using voom followed by lmFit functions, separately on each M imputed dataset within each gene bin, 4) Un-binning the gene sets and stacking the M sets of model results before applying the squeezeVar function to apply a variance shrinking Bayesian procedure to each M set of model results, 5) Pooling the results with Rubins’ rules to produce combined coefficients, standard errors, and P-values, and 6) Adjusting P-values for multiplicity to account for false discovery rate (FDR).
Author: Brennan Baker [aut, cre] 
, Sheela Sathyanarayana [aut], Adam Szpiro [aut], James MacDonald [aut], Alison Paquette [aut]
Maintainer: Brennan Baker <brennanhilton at gmail.com>
citation("RNAseqCovarImpute")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RNAseqCovarImpute")
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("RNAseqCovarImpute")| Example Data for RNAseqCovarImpute | HTML | R Script |
| Impute Covariate Data in RNA-sequencing Studies | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.18 (R-4.3) (0.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.3.0) |
| Imports | Biobase, BiocParallel, stats, limma, dplyr, magrittr, rlang, edgeR, foreach, mice |
| System Requirements | |
| URL | https://github.com/brennanhilton/RNAseqCovarImpute |
| Bug Reports | https://github.com/brennanhilton/RNAseqCovarImpute/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, tidyr, stringr, testthat (>= 3.0.0) |
| 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 | RNAseqCovarImpute_1.0.2.tar.gz |
| Windows Binary | RNAseqCovarImpute_1.0.2.zip |
| macOS Binary (x86_64) | RNAseqCovarImpute_1.0.2.tgz |
| macOS Binary (arm64) | RNAseqCovarImpute_1.0.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RNAseqCovarImpute |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RNAseqCovarImpute |
| Bioc Package Browser | https://code.bioconductor.org/browse/RNAseqCovarImpute/ |
| Package Short Url | https://bioconductor.org/packages/RNAseqCovarImpute/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.18 | Source Archive |