ccImpute
This is the development version of ccImpute; for the stable release version, see 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: Development (3.24)
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.
Author: Marcin Malec [cre, aut]
, Parichit Sharma [aut]
, Hasan Kurban [aut]
, Mehmet Dalkilic [aut]
Maintainer: Marcin Malec <mamalec at iu.edu>
citation("ccImpute")):
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("ccImpute")
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("ccImpute")| ccImpute package manual | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DimensionReduction, PrincipalComponent, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | GPL-3 |
| Depends | |
| Imports | Rcpp, sparseMatrixStats, stats, BiocParallel, irlba, SingleCellExperiment, Matrix, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/khazum/ccImpute/ |
| Bug Reports | https://github.com/khazum/ccImpute/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, mclust, testthat (>= 3.0.0), splatter |
| Linking To | Rcpp, RcppEigen |
| 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 | ccImpute_1.15.0.tar.gz |
| Windows Binary (x86_64) | ccImpute_1.15.0.zip |
| macOS Binary (big-sur-x86_64) | ccImpute_1.15.0.tgz |
| macOS Binary (sonoma-arm64) | ccImpute_1.15.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ccImpute |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ccImpute |
| Bioc Package Browser | https://code.bioconductor.org/browse/ccImpute/ |
| Package Short Url | https://bioconductor.org/packages/ccImpute/ |
| Package Downloads Report | Download Stats |