ISLET
Individual-Specific ceLl typE referencing Tool
Bioconductor version: 3.24 · Package version: 1.15.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ISLET")Details
| Maintainer | Hao Feng <hxf155@case.edu> |
| Author | Hao Feng [aut, cre] (ORCID: <https://orcid.org/0000-0003-2243-9949>), Qian Li [aut], Guanqun Meng [aut] |
| License | GPL-2 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, DifferentialMethylation, GeneExpression, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/ISLET/ |
Citation
From within R, enter citation("ISLET"):
Hao Feng, Qian Li, Guanqun Meng. ISLET: Individual-Specific ceLl typE referencing Tool. doi:10.18129/B9.bioc.ISLET, R package version 1.15.0, https://bioconductor.org/packages/ISLET.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ISLET_1.15.0.tar.gz |
| Windows binary (x86_64) | ISLET_1.15.0.zip |
| macOS binary (arm64) | ISLET_1.15.0.tgz |
| macOS binary (x86_64) | ISLET_1.15.0.tgz |
Dependencies
Depends: R (>= 4.2.0), Matrix, parallel, BiocParallel, SummarizedExperiment, BiocGenerics, lme4, nnls
Imports: stats, methods, purrr, abind
Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr