ISLET

DOI: 10.18129/B9.bioc.ISLET    

This is the development version of ISLET; to use it, please install the devel version of Bioconductor.

Individual-Specific ceLl typE referencing Tool

Bioconductor version: Development (3.16)

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. It can also conduct test to identify cell-type-specific differential expression (csDE) genes.

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

Maintainer: Hao Feng <hxf155 at case.edu>

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

Installation

To install this package, start R (version "4.2") 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")

 

HTML R Script Individual-specific and cell-type-specific deconvolution using ISLET
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, DifferentialMethylation, GeneExpression, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 0.99.8
In Bioconductor since BioC 3.16 (R-4.2)
License GPL-2
Depends R (>= 4.1.0), Matrix, parallel, BiocParallel, SummarizedExperiment, BiocGenerics
Imports stats, methods
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, htmltools, RUnit
SystemRequirements
Enhances
URL
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 ISLET_0.99.8.tar.gz
Windows Binary ISLET_0.99.8.zip
macOS Binary (x86_64) ISLET_0.99.8.tgz
macOS Binary (arm64) ISLET_0.99.8.tgz
Source Repository git clone https://git.bioconductor.org/packages/ISLET
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ISLET
Package Short Url https://bioconductor.org/packages/ISLET/
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