ISLET
This is thereleased version of ISLET; for the devel version, seeISLET.
Individual-Specific ceLl typE referencing Tool
Bioconductor version: Release (3.22)
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: 0000-0003-2243-9949, Qian Li [aut], Guanqun Meng [aut]
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")BiocManager::install("ISLET")For older versions of R, please refer to the appropriateBioconductor 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 | 1.12.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3 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 | |
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| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | ISLET_1.12.0.tar.gz |
| Windows Binary (x86_64) | ISLET_1.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | ISLET_1.12.0.tgz |
| macOS Binary (arm64) | ISLET_1.12.0.tgz |
| 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 |