Package: ISLET
Type: Package
Title: Individual-Specific ceLl typE referencing Tool
Version: 1.12.0
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
Config/pak/sysreqs: cmake make zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:18:35 UTC
RemoteUrl: https://github.com/bioc/ISLET
RemoteRef: RELEASE_3_22
RemoteSha: ab9b7852c589507a3996cac30dcdfa3eea3c8740
NeedsCompilation: no
Packaged: 2026-03-05 07:59:51 UTC; root
Author: Hao Feng [aut, cre] (ORCID: <https://orcid.org/0000-0003-2243-9949>),
  Qian Li [aut],
  Guanqun Meng [aut]
Maintainer: Hao Feng <hxf155@case.edu>
Built: R 4.5.2; ; 2026-03-05 08:01:43 UTC; windows
