ILoReg

DOI: 10.18129/B9.bioc.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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	ILoReg package manual
PDF		Reference Manual
Text		NEWS

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) (1 year)
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
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/elolab/ILoReg
BugReports	https://github.com/elolab/ILoReg/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
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
Package Short Url	https://bioconductor.org/packages/ILoReg/
Package Downloads Report	Download Stats