ILoReg
This is the development version of ILoReg; for the stable release version, see ILoReg.
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
Bioconductor version: Development (3.24)
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("ILoReg")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("ILoReg")
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("ILoReg")| ILoReg package manual | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DataRepresentation, DifferentialExpression, DimensionReduction, GeneExpression, RNASeq, SingleCell, Software, Transcription, Transcriptomics, Visualization |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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 |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| Linking To | |
| 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 | ILoReg_1.23.0.tar.gz |
| Windows Binary (x86_64) | ILoReg_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | ILoReg_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | ILoReg_1.23.0.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/ |
| Package Downloads Report | Download Stats |