ccImpute
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)
Bioconductor version: 3.23 · Package version: 1.14.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ccImpute")Details
| Maintainer | Marcin Malec <mamalec@iu.edu> |
| 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] |
| License | GPL-3 |
| URL | https://github.com/khazum/ccImpute/ |
| Bug Reports | https://github.com/khazum/ccImpute/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, DimensionReduction, PrincipalComponent, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/ccImpute/ |
Citation
From within R, enter citation("ccImpute"):
Marcin Malec, Parichit Sharma, Hasan Kurban, Mehmet Dalkilic. ccImpute: 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). doi:10.18129/B9.bioc.ccImpute, R package version 1.14.0, https://bioconductor.org/packages/ccImpute.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ccImpute_1.14.0.tar.gz |
| Windows binary (x86_64) | ccImpute_1.14.0.zip |
| macOS binary (arm64) | ccImpute_1.14.0.tgz |
| macOS binary (x86_64) | ccImpute_1.14.0.tgz |
Dependencies
Imports: Rcpp, sparseMatrixStats, stats, BiocParallel, irlba, SingleCellExperiment, Matrix, SummarizedExperiment
Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, mclust, testthat (>= 3.0.0), splatter