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:
Maintainer: Hao Feng <hxf155 at case.edu>
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 | ||
| NEWS | Text |
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 |
See More
| 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) | ISLET_1.9.0.zip |
| macOS Binary (x86_64) | ISLET_1.9.0.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 |