ADImpute

DOI: 10.18129/B9.bioc.ADImpute    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see ADImpute.

Adaptive Dropout Imputer (ADImpute)

Bioconductor version: 3.12

Single-cell RNA sequencing (scRNA-seq) methods are typically unable to quantify the expression levels of all genes in a cell, creating a need for the computational prediction of missing values (‘dropout imputation’). Most existing dropout imputation methods are limited in the sense that they exclusively use the scRNA-seq dataset at hand and do not exploit external gene-gene relationship information. Here we propose two novel methods: a gene regulatory network-based approach using gene-gene relationships learnt from external data and a baseline approach corresponding to a sample-wide average. ADImpute can implement these novel methods and also combine them with existing imputation methods (currently supported: DrImpute, SAVER). ADImpute can learn the best performing method per gene and combine the results from different methods into an ensemble.

Author: Ana Carolina Leote [cre, aut]

Maintainer: Ana Carolina Leote <anacarolinaleote at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ADImpute")

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("ADImpute")

 

HTML	R Script	ADImpute tutorial
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, Network, Preprocessing, Sequencing, SingleCell, Software, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.12 (R-4.0) (0.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.0)
Imports	ArgumentCheck, BiocParallel, data.table, DrImpute, kernlab, MASS, Matrix, methods, rsvd, S4Vectors, SAVER, SingleCellExperiment, stats, SummarizedExperiment, utils
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/anacarolinaleote/ADImpute/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	ADImpute_1.0.0.tar.gz
Windows Binary	ADImpute_1.0.0.zip
macOS 10.13 (High Sierra)	ADImpute_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ADImpute
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ADImpute
Package Short Url	https://bioconductor.org/packages/ADImpute/
Package Downloads Report	Download Stats