ILoReg
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see ILoReg.
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
Bioconductor version: 3.13
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")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.2.0 |
| 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 | |
| URL | https://github.com/elolab/ILoReg |
| Bug Reports | https://github.com/elolab/ILoReg/issues |
See More
| Suggests | knitr, rmarkdown |
| 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_1.2.0.tar.gz |
| Windows Binary | ILoReg_1.2.0.zip |
| macOS 10.13 (High Sierra) | ILoReg_1.2.0.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 |
| Old Source Packages for BioC 3.13 | Source Archive |