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ISLET

This is the development version of ISLET; for the stable release version, see ISLET.

Individual-Specific ceLl typE referencing Tool


Bioconductor version: Development (3.19)

ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis and conduct test to identify cell-type-specific differential expression (csDE) genes. It also improves estimated cell type mixture proportions by integrating personalized reference panels.

Author: Hao Feng [aut, cre] , Qian Li [aut], Guanqun Meng [aut]

Maintainer: Hao Feng <hxf155 at case.edu>

Citation (from within R, enter citation("ISLET")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ISLET")

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("ISLET")
Individual-specific and cell-type-specific deconvolution using ISLET HTML R Script
Reference Manual PDF

Details

biocViews DifferentialExpression, DifferentialMethylation, GeneExpression, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.5.1
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License GPL-2
Depends R (>= 4.2.0), Matrix, parallel, BiocParallel, SummarizedExperiment, BiocGenerics, lme4, nnls
Imports stats, methods, purrr, abind
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ISLET_1.5.1.tar.gz
Windows Binary
macOS Binary (x86_64) ISLET_1.5.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/ISLET
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ISLET
Bioc Package Browser https://code.bioconductor.org/browse/ISLET/
Package Short Url https://bioconductor.org/packages/ISLET/
Package Downloads Report Download Stats