ADImpute

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see ADImpute.

Adaptive Dropout Imputer (ADImpute)


Bioconductor version: 3.13

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 "4.1") and enter:


if (!require("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")
ADImpute tutorial HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, Network, Preprocessing, Sequencing, SingleCell, Software, Transcriptomics
Version 1.2.0
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
Links To Me
Build Report Build Report

Package Archives

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

Source Package ADImpute_1.2.0.tar.gz
Windows Binary ADImpute_1.2.0.zip
macOS 10.13 (High Sierra) ADImpute_1.2.0.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
Old Source Packages for BioC 3.13 Source Archive