Package: lute 1.1.0
Sean K Maden
lute: Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments
Provides a framework for adjustment on cell type size when performing bulk transcripomics deconvolution. The main framework function provides a means of reference normalization using cell size scale factors. It allows for marker selection and deconvolution using non-negative least squares (NNLS) by default. The framework is extensible for other marker selection and deconvolution algorithms, and users may reuse the generics, methods, and classes for these when developing new algorithms.
Authors:
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lute.pdf |lute.html✨
lute/json (API)
NEWS
| # Install 'lute' in R: |
| install.packages('lute', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/metamaden/lute/issues
On BioConductor:lute-1.1.0(bioc 3.20)lute-1.0.0(bioc 3.19)
Last updated 7 days agofrom:6035ac3d47
Exports:bisqueParamcellProportionsPredictionsdeconvolutioneset_to_sceeset_to_sefindmarkersParamget_celltypes_from_sceget_csf_referenceget_eset_from_matrixgetDeconvolutionExampleDatagetDeconvolutionExampleDataBisquegetDeconvolutionExampleDataSCDCindependentbulkParamluteluteSupportedDeconvolutionAlgorithmsnew_workflow_tablennlsParamparseDeconvolutionPredictionsResultsproportionsVectorsListrandomMarkersVectorsListrandomSingleCellExperimentreferencebasedParamreferenceFromSingleCellExperimentrmsermseTestsce_to_esetsce_to_sese_to_esetse_to_sceshowtypemarkerstypemarkersParamypb_from_scez_matrix_from_sce
Dependencies:abindaskpassbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblustercliclustercodetoolscolorspacecpp11crayoncurlDelayedArrayDelayedMatrixStatsdplyrdqrngedgeRfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrigraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmetapodmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcppRcppHNSWrlangrsvdS4ArraysS4VectorsScaledMatrixscalesscranscuttleSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
lute algorithm class definitions and uses
Rendered fromlute_algorithm_classes.Rmdusingknitr::rmarkdownon Jul 04 2024.Last update: 2024-07-03
Started: 2024-01-25
Pseudobulk cell size rescaling example
Rendered fromlute_pseudobulk_example.Rmdusingknitr::rmarkdownon Jul 04 2024.Last update: 2024-03-19
Started: 2023-10-17
The lute user's guide
Rendered fromlute_users_guide.Rmdusingknitr::rmarkdownon Jul 04 2024.Last update: 2024-07-03
Started: 2023-03-28
