RNAseqCovarImpute

DOI: 10.18129/B9.bioc.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>

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")

 

HTML	R Script	Example Data for RNAseqCovarImpute
HTML	R Script	Impute Covariate Data in RNA-sequencing Studies
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software
Version	1.0.2
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	GPL-3
Depends	R (>= 4.3.0)
Imports	Biobase, BiocParallel, stats, limma, dplyr, magrittr, rlang, edgeR, foreach, mice
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, tidyr, stringr, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/brennanhilton/RNAseqCovarImpute
BugReports	https://github.com/brennanhilton/RNAseqCovarImpute/issues
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	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