This is the development version of ADImpute; for the stable release version, see ADImpute.
Adaptive Dropout Imputer (ADImpute)Bioconductor version: Development (3.22)
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 (âdropout imputationâ). 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] ORCID: 0000-0003-0879-328X
Maintainer: Ana Carolina Leote <anacarolinaleote at gmail.com>
Citation (from within R, entercitation("ADImpute")): Installation
To install this package, start R (version "4.5") 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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ADImpute")Follow Installation instructions to use this package in your R session.
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