Package: ISLET
Type: Package
Title: Individual-Specific ceLl typE referencing Tool
Version: 1.6.0
Date: 2023-09-15
Authors@R: c(person("Hao", "Feng", role = c("aut", "cre"),email = "hxf155@case.edu",comment=c(ORCID="0000-0003-2243-9949")),
             person("Qian", "Li", role = "aut",email = "Qian.Li@STJUDE.ORG"),
             person("Guanqun", "Meng", role = "aut",email = "gxm324@case.edu"))
Description: 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.
License: GPL-2
Depends: R(>= 4.2.0), Matrix, parallel, BiocParallel,
        SummarizedExperiment, BiocGenerics, lme4, nnls
Imports: stats, methods, purrr, abind
Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr
Collate: utils.R dataprep.R dataprep_slope.R islet.est.R islet.solve.R
        islet.test.R AllClasses.R show-methods.R imply_prep.R imply.R
biocViews: Software, RNASeq, Transcriptomics, Transcription,
        Sequencing, GeneExpression, DifferentialExpression,
        DifferentialMethylation
Encoding: UTF-8
LazyData: false
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ISLET
git_branch: RELEASE_3_19
git_last_commit: b173ae9
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-01 23:45:44 UTC; biocbuild
Author: Hao Feng [aut, cre] (<https://orcid.org/0000-0003-2243-9949>),
  Qian Li [aut],
  Guanqun Meng [aut]
Maintainer: Hao Feng <hxf155@case.edu>
Built: R 4.4.0; ; 2024-05-02 13:00:09 UTC; windows
