ILoReg

DOI: 10.18129/B9.bioc.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 (3.13)

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 (from within R, enter citation("ILoReg")):

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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")

 

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 1.1.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
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_1.1.0.tar.gz
Windows Binary ILoReg_1.1.0.zip
macOS 10.13 (High Sierra) ILoReg_1.1.0.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

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