Package: ccImpute
Type: Package
Title: ccImpute: an accurate and scalable consensus clustering based
        approach to impute dropout events in the single-cell RNA-seq
        data (https://doi.org/10.1186/s12859-022-04814-8)
Version: 1.13.0
Authors@R: c(
	person("Marcin", "Malec",
  	email = "mamalec@iu.edu",
  	role = c("cre", "aut"),
  	comment = c(ORCID = "0000-0002-2354-513X")),
  	person("Parichit", "Sharma",
  	email = "parishar@iu.edu",
  	role = c("aut"),
  	comment = c(ORCID = "0000-0003-0822-1089")),
  	person("Hasan", "Kurban",
  	email = "hasan.kurban@tamu.edu",
  	role = c("aut"),
  	comment = c(ORCID = "0000-0003-3142-2866")),
  	person("Mehmet", "Dalkilic",
  	email = "dalkilic@indiana.edu",
  	role = c("aut")))
Description: Dropout events make the lowly expressed genes
        indistinguishable from true zero expression and different than
        the low expression present in cells of the same type. This
        issue makes any subsequent downstream analysis difficult.
        ccImpute is an imputation algorithm that uses cell similarity
        established by consensus clustering to impute the most probable
        dropout events in the scRNA-seq datasets. ccImpute demonstrated
        performance which exceeds the performance of existing
        imputation approaches while introducing the least amount of new
        noise as measured by clustering performance characteristics on
        datasets with known cell identities.
License: GPL-3
Imports: Rcpp, sparseMatrixStats, stats, BiocParallel, irlba,
        SingleCellExperiment, Matrix, SummarizedExperiment
LinkingTo: Rcpp, RcppEigen
Encoding: UTF-8
BugReports: https://github.com/khazum/ccImpute/issues
URL: https://github.com/khazum/ccImpute/
RoxygenNote: 7.3.2
biocViews: SingleCell, Sequencing, PrincipalComponent,
        DimensionReduction, Clustering, RNASeq, Transcriptomics
biocType: Software
Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater,
        mclust, testthat (>= 3.0.0), splatter
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:19:37 UTC
RemoteUrl: https://github.com/bioc/ccImpute
RemoteRef: HEAD
RemoteSha: 076b708567142060696fa0ed973b419d215bde5f
NeedsCompilation: yes
Packaged: 2026-01-09 21:11:14 UTC; root
Author: Marcin Malec [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-2354-513X>),
  Parichit Sharma [aut] (ORCID: <https://orcid.org/0000-0003-0822-1089>),
  Hasan Kurban [aut] (ORCID: <https://orcid.org/0000-0003-3142-2866>),
  Mehmet Dalkilic [aut]
Maintainer: Marcin Malec <mamalec@iu.edu>
Built: R 4.6.0; x86_64-w64-mingw32; 2026-01-09 21:14:40 UTC; windows
Archs: x64
