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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 (3.18)

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]

Maintainer: Marcin Malec <mamalec at iu.edu>

Citation (from within R, enter citation("ccImpute")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 PDF
NEWS Text

Details

biocViews Clustering, DimensionReduction, PrincipalComponent, RNASeq, SingleCell, Software, Transcriptomics
Version 1.3.0
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
License GPL-3
Depends
Imports Rcpp, matrixStats, stats, SIMLR, BiocParallel
Linking To Rcpp, RcppEigen
Suggests knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, SingleCellExperiment, mclust, testthat (>= 3.0.0)
System Requirements
Enhances
URL
Bug Reports https://github.com/khazum/ccImpute/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ccImpute_1.3.0.tar.gz
Windows Binary ccImpute_1.3.0.zip (64-bit only)
macOS Binary (x86_64) ccImpute_1.3.0.tgz
macOS Binary (arm64) ccImpute_1.3.0.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