Package: ISLET 1.7.0

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_1.7.0.tar.gz
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ISLET_1.7.0.tgz(r-4.4-any)ISLET_1.7.0.tgz(r-4.3-any)
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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'))

Datasets:

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

On BioConductor:ISLET-1.7.0(bioc 3.20)ISLET-1.6.0(bioc 3.19)

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

bioconductor-package

8 exports 0.61 score 75 dependencies

Last updated 2 months agofrom:34b1288955

Exports:caseEst ctrlEst dataPrep dataPrepSlope imply implyDataPrep isletSolve isletTest

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel boot brio callr cli codetools cpp11 crayon curl DelayedArray desc diffobj digest evaluate fansi formatR fs futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges jsonlite lambda.r lattice lifecycle lme4 magrittr MASS Matrix MatrixGenerics matrixStats mime minqa nlme nloptr nnls openssl pillar pkgbuild pkgconfig pkgload praise processx ps purrr R6 Rcpp RcppEigen rematch2 rlang rprojroot S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys testthat tibble UCSC.utils utf8 vctrs waldo withr XVector zlibbioc

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

Hao Feng, Qian Li, Guanqun Meng

Rendered fromISLET.Rmdusingknitr::rmarkdownon Jun 17 2024.

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

Help page	Topics
ISLET reference estimation results extraction	caseEst
ISLET reference estimation results extraction	ctrlEst
Data preparation step utility function before using ISLET	dataPrep
Data preparation function specifically for slope effect testing	dataPrepSlope
ISLET deconvolution example raw input data	GE600 GE600_se
ISLET example datasets for slope variable testing in csDE	GE600age GE600age_se
_imply_: _imp_roving ce_l_l-t_y_pe deconvolution using personalized reference	imply
Data preparation step utility function before using imply	implyDataPrep
Solving individual-specific and cell-type-specific reference panels	isletSolve
Testing for cell-type-specific Differential Expression (csDE) genes	isletTest

Package: ISLET 1.7.0

ISLET: Individual-Specific ceLl typE referencing Tool

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

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)