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ADImpute

This is the development version of ADImpute; for the stable release version, see ADImpute.

Adaptive Dropout Imputer (ADImpute)


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("ADImpute")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
ADImpute tutorial HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews GeneExpression, Network, Preprocessing, Sequencing, SingleCell, Software, Transcriptomics
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3 + file LICENSE
Depends R (>= 4.0)
Imports checkmate, BiocParallel, data.table, DrImpute, kernlab, MASS, Matrix, methods, rsvd, S4Vectors, SAVER, SingleCellExperiment, stats, SummarizedExperiment, utils
System Requirements
URL
Bug Reports https://github.com/anacarolinaleote/ADImpute/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ADImpute_1.13.0.tar.gz
Windows Binary ADImpute_1.13.0.zip
macOS Binary (x86_64) ADImpute_1.13.0.tgz
macOS Binary (arm64) ADImpute_1.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ADImpute
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ADImpute
Bioc Package Browser https://code.bioconductor.org/browse/ADImpute/
Package Short Url https://bioconductor.org/packages/ADImpute/
Package Downloads Report Download Stats