Package: MICSQTL 1.5.0

Qian Li

MICSQTL: MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)

Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.

Authors:Yue Pan [aut], Qian Li [aut, cre], Iain Carmichael [ctb]

MICSQTL_1.5.0.tar.gz
MICSQTL_1.5.0.zip(r-4.5)MICSQTL_1.5.0.zip(r-4.4)MICSQTL_1.5.0.zip(r-4.3)
MICSQTL_1.5.0.tgz(r-4.4-any)MICSQTL_1.5.0.tgz(r-4.3-any)
MICSQTL_1.5.0.tar.gz(r-4.5-noble)MICSQTL_1.5.0.tar.gz(r-4.4-noble)
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MICSQTL.pdf |MICSQTL.html✨
MICSQTL/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/yuepan027/micsqtl/issues

Datasets:
  • se - Example data

On BioConductor:MICSQTL-1.5.0(bioc 3.21)MICSQTL-1.4.0(bioc 3.20)

geneexpressiongeneticsproteomicsrnaseqsequencingsinglecellsoftwarevisualizationcellbasedassayscoverage

4.30 score 3 scripts 112 downloads 4 exports 135 dependencies

Last updated 2 months agofrom:3dd556e725. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winOKDec 18 2024
R-4.5-linuxOKDec 18 2024
R-4.4-winOKDec 18 2024
R-4.4-macOKDec 18 2024
R-4.3-winOKDec 18 2024
R-4.3-macOKDec 18 2024

Exports:ajive_decompcsQTLdeconvfeature_filter

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocParallelbootbroomcarcarDataclassclicodetoolscolorspaceconfigcorpcorcorrplotcowplotcpp11crayoncurldata.tableDelayedArrayDerivdirmultdoBydoParalleldplyre1071EpiDISHfansifarverforcatsforeachformatRFormulafutile.loggerfutile.optionsgdatagenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGGallyggplot2ggpubrggrepelggridgesggsciggsignifggstatsgluegmodelsgridExtragtablegtoolshmshttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelimmalme4locfdrmagrittrMASSMatrixmatrixcalcMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnnlsnumDerivopensslpatchworkpbapplypbkrtestpillarpkgconfigplyrpolynompracmaprettyunitsprogressproxypurrrquadprogquantregR6RColorBrewerRcppRcppEigenrlangrstatixrsvdS4ArraysS4VectorsscalessnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsysTCAtibbletidyrtidyselectTOASTUCSC.utilsutf8vctrsviridisLitewithrXVectoryamlzlibbioc

MICSQTL: Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci

Yue Pan, Qian Li

Rendered fromMICSQTL.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-03-08
Started: 2023-04-21