Package: ISLET 1.15.0

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_1.15.0.tar.gz
ISLET_1.15.0.zip(r-4.7)ISLET_1.15.0.zip(r-4.6)ISLET_1.15.0.zip(r-4.5)
ISLET_1.15.0.tgz(r-4.6-any)ISLET_1.15.0.tgz(r-4.5-any)
ISLET_1.15.0.tar.gz(r-4.7-any)ISLET_1.15.0.tar.gz(r-4.6-any)
ISLET_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ISLET/json (API)

# 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-1.15.0(bioc 3.24)ISLET-1.14.0(bioc 3.23)

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

software rnaseq transcriptomics transcription sequencing geneexpression differentialexpression differentialmethylation

4.15 score 14 scripts 8 exports 45 dependencies

Last updated from:a533001d01. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	178
linux-devel-x86_64	OK	495
source / vignettes	OK	312
linux-release-x86_64	OK	447
macos-release-arm64	OK	391
macos-oldrel-arm64	OK	359
windows-devel	OK	647
windows-release	OK	652
windows-oldrel	OK	634
wasm-release	OK	145

Exports:caseEst ctrlEst dataPrep dataPrepSlope imply implyDataPrep isletSolve isletTest

Dependencies:abind BH Biobase BiocGenerics BiocParallel boot cli codetools cpp11 DelayedArray formatR futile.logger futile.options generics GenomicRanges glue IRanges lambda.r lattice lifecycle lme4 magrittr MASS Matrix MatrixGenerics matrixStats minqa nlme nloptr nnls purrr rbibutils Rcpp RcppEigen Rdpack reformulas rlang S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment vctrs XVector

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

Rendered fromISLET.Rmdusingknitr::rmarkdown

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 1.15.0

ISLET: Individual-Specific ceLl typE referencing Tool

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)