ADImpute
This is the development version of ADImpute; for the stable release version, see ADImpute.
Adaptive Dropout Imputer (ADImpute)
Bioconductor version: Development (3.24)
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("ADImpute")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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_1.23.0.tar.gz |
| Windows Binary (x86_64) | ADImpute_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | ADImpute_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | ADImpute_1.23.0.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 |