ISLET

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

Individual-Specific ceLl typE referencing Tool

Bioconductor version: Development (3.21)

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] (ORCID: ), 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 "4.5") 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
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, DifferentialMethylation, GeneExpression, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version	1.9.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 years)
License	GPL-2
Depends	R (>= 4.2.0), Matrix, parallel, BiocParallel, SummarizedExperiment, BiocGenerics, lme4, nnls
Imports	stats, methods, purrr, abind
System Requirements
URL

Suggests	BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr
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	ISLET_1.9.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
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