ILoReg
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
Bioconductor version: 3.24 · Package version: 1.23.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ILoReg")Details
| Maintainer | Johannes Smolander <johannes.smolander@gmail.com> |
| Author | Johannes Smolander [cre, aut], Sini Junttila [aut], Mikko S Venäläinen [aut], Laura L Elo [aut] |
| License | GPL-3 |
| URL | https://github.com/elolab/ILoReg |
| Bug Reports | https://github.com/elolab/ILoReg/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, DataRepresentation, DifferentialExpression, DimensionReduction, GeneExpression, RNASeq, SingleCell, Software, Transcription, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/ILoReg/ |
Citation
From within R, enter citation("ILoReg"):
Johannes Smolander, Sini Junttila, Mikko S Venäläinen, Laura L Elo. ILoReg: ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data. doi:10.18129/B9.bioc.ILoReg, R package version 1.23.0, https://bioconductor.org/packages/ILoReg.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ILoReg_1.23.0.tar.gz |
| Windows binary (x86_64) | ILoReg_1.23.0.zip |
| macOS binary (arm64) | ILoReg_1.23.0.tgz |
| macOS binary (x86_64) | ILoReg_1.23.0.tgz |
Dependencies
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