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 (3.21)

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] (ORCID: ), Parichit Sharma [aut] (ORCID: ), Hasan Kurban [aut] (ORCID: ), Mehmet Dalkilic [aut]

Maintainer: Marcin Malec <mamalec at iu.edu>

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, DimensionReduction, PrincipalComponent, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.9.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 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

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_1.9.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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