Package: ADImpute
Type: Package
Title: Adaptive Dropout Imputer (ADImpute)
Version: 1.21.0
Description: 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.
Authors@R: person("Ana Carolina", "Leote", email = "anacarolinaleote@gmail.com",
           role = c("cre","aut"), comment = c(ORCID = "0000-0003-0879-328X"))
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0)
Imports: checkmate, BiocParallel, data.table, DrImpute, kernlab, MASS,
        Matrix, methods, rsvd, S4Vectors, SAVER, SingleCellExperiment,
        stats, SummarizedExperiment, utils
Suggests: BiocStyle, knitr, rmarkdown, testthat
biocViews: GeneExpression, Network, Preprocessing, Sequencing,
        SingleCell, Transcriptomics
RoxygenNote: 7.1.1
VignetteBuilder: knitr
BugReports: https://github.com/anacarolinaleote/ADImpute/issues
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:04:05 UTC
RemoteUrl: https://github.com/bioc/ADImpute
RemoteRef: HEAD
RemoteSha: 8a9fa739aa644fb9b7ede35dceef248111c32a3c
NeedsCompilation: no
Packaged: 2025-10-30 03:30:16 UTC; root
Author: Ana Carolina Leote [cre, aut] (ORCID:
    <https://orcid.org/0000-0003-0879-328X>)
Maintainer: Ana Carolina Leote <anacarolinaleote@gmail.com>
Built: R 4.6.0; ; 2025-10-30 03:32:31 UTC; windows
