Package: ISLET 1.9.0

Hao Feng

ISLET: Individual-Specific ceLl typE referencing Tool

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.

Authors:Hao Feng [aut, cre], Qian Li [aut], Guanqun Meng [aut]

ISLET_1.9.0.tar.gz
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ISLET.pdf |ISLET.html✨
ISLET/json (API)
NEWS

# Install 'ISLET' in R:
install.packages('ISLET', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • GE600_se - ISLET deconvolution example raw input data
  • GE600age_se - ISLET example datasets for slope variable testing in csDE

On BioConductor:ISLET-1.9.0(bioc 3.21)ISLET-1.8.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwarernaseqtranscriptomicstranscriptionsequencinggeneexpressiondifferentialexpressiondifferentialmethylation

4.18 score 9 scripts 158 downloads 8 exports 54 dependencies

Last updated 2 months agofrom:7137eb91dd. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winOKNov 29 2024
R-4.5-linuxOKNov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:caseEstctrlEstdataPrepdataPrepSlopeimplyimplyDataPrepisletSolveisletTest

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelbootclicodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsmimeminqanlmenloptrnnlsopensslpurrrR6RcppRcppEigenrlangS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc

Individual-specific and cell-type-specific deconvolution using ISLET

Hao Feng, Qian Li, Guanqun Meng

Rendered fromISLET.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-09-15
Started: 2022-06-15