Registration Open for Bioc2024 July 24-26


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

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") 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 1.14.0
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
Bug Reports
See More
Suggests knitr, rmarkdown, BiocStyle
Linking To
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 ILoReg_1.14.0.tar.gz
Windows Binary
macOS Binary (x86_64) ILoReg_1.14.0.tgz
macOS Binary (arm64) ILoReg_1.14.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats