Package: ILoReg
Type: Package
Title: ILoReg: a tool for high-resolution cell population
        identification from scRNA-Seq data
Version: 1.23.0
Description: 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.
Authors@R: c(person("Johannes", "Smolander",
             email = "johannes.smolander@gmail.com",
             role=c("cre", "aut")),
             person("Sini", "Junttila",
             role=c("aut")),
             person("Mikko S", "Venäläinen",
             role=c("aut")),
             person("Laura L", "Elo",
             role=c("aut")))
License: GPL-3
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
Depends: R (>= 4.0.0)
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
biocViews: SingleCell, Software, Clustering, DimensionReduction,
        RNASeq, Visualization, Transcriptomics, DataRepresentation,
        DifferentialExpression, Transcription, GeneExpression
NeedsCompilation: no
URL: https://github.com/elolab/ILoReg
BugReports: https://github.com/elolab/ILoReg/issues
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libuv1-dev
        libssl-dev python3 libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:53:15 UTC
RemoteUrl: https://github.com/bioc/ILoReg
RemoteRef: HEAD
RemoteSha: 5f0e20dca622c5b9fbe39f5920703fb4fc7375ae
Packaged: 2026-05-30 07:56:40 UTC; root
Author: Johannes Smolander [cre, aut],
  Sini Junttila [aut],
  Mikko S Venäläinen [aut],
  Laura L Elo [aut]
Maintainer: Johannes Smolander <johannes.smolander@gmail.com>
Built: R 4.6.0; ; 2026-05-30 07:58:31 UTC; windows
