ADImpute
This is the development version of ADImpute; for the stable release version, see ADImpute.
Adaptive Dropout Imputer (ADImpute)
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Ana Carolina Leote <anacarolinaleote at gmail.com>
citation("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.
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 | ||
| LICENSE | Text |
Details
| biocViews | GeneExpression, Network, Preprocessing, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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_1.17.0.tar.gz |
| Windows Binary (x86_64) | ADImpute_1.17.0.zip |
| macOS Binary (x86_64) | ADImpute_1.17.0.tgz |
| macOS Binary (arm64) | ADImpute_1.17.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ADImpute |
| Source Repository (Developer Access) | git clone [email protected]:packages/ADImpute |
| Bioc Package Browser | https://code.bioconductor.org/browse/ADImpute/ |
| Package Short Url | https://bioconductor.org/packages/ADImpute/ |
| Package Downloads Report | Download Stats |