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ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

Bioconductor version: Release (3.18)

ILoReg is a tool for identification of cell populations from scRNA-seq data. In particular, ILoReg is useful for finding cell populations with subtle transcriptomic differences. The method utilizes a self-supervised learning method, called Iteratitive Clustering Projection (ICP), to find cluster probabilities, which are used in noise reduction prior to PCA and the subsequent hierarchical clustering and t-SNE steps. Additionally, functions for differential expression analysis to find gene markers for the populations and gene expression visualization are provided.

Author: Johannes Smolander [cre, aut], Sini Junttila [aut], Mikko S Venäläinen [aut], Laura L Elo [aut]

Maintainer: Johannes Smolander <johannes.smolander at gmail.com>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

ILoReg package manual HTML R Script
Reference Manual PDF


biocViews Clustering, DataRepresentation, DifferentialExpression, DimensionReduction, GeneExpression, RNASeq, SingleCell, Software, Transcription, Transcriptomics, Visualization
Version 1.12.1
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.0.0)
Imports Matrix, parallel, foreach, aricode, LiblineaR, SparseM, ggplot2, cowplot, RSpectra, umap, Rtsne, fastcluster, parallelDist, cluster, dendextend, DescTools, plyr, scales, pheatmap, reshape2, dplyr, doRNG, SingleCellExperiment, SummarizedExperiment, S4Vectors, methods, stats, doSNOW, utils
System Requirements
URL https://github.com/elolab/ILoReg
Bug Reports https://github.com/elolab/ILoReg/issues
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Suggests knitr, rmarkdown, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package ILoReg_1.12.1.tar.gz
Windows Binary ILoReg_1.12.1.zip
macOS Binary (x86_64) ILoReg_1.12.1.tgz
macOS Binary (arm64) ILoReg_1.12.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/ILoReg
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ILoReg
Bioc Package Browser https://code.bioconductor.org/browse/ILoReg/
Package Short Url https://bioconductor.org/packages/ILoReg/
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