Package: airpart 1.13.0
Wancen Mu
airpart: Differential cell-type-specific allelic imbalance
Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of a generalized fused lasso with binomial observations of allelic counts to partition cell types by their allelic imbalance. Alternatively, a nonparametric method for partitioning cell types is offered. The package includes a number of visualizations and quality control functions for examining single cell allelic imbalance datasets.
Authors:
airpart_1.13.0.tar.gz
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airpart.pdf |airpart.html✨
airpart/json (API)
NEWS
| # Install 'airpart' in R: |
| install.packages('airpart', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wancen/airpart/issues
On BioConductor:airpart-1.13.0(bioc 3.20)airpart-1.12.0(bioc 3.19)
Last updated 2 months agofrom:76baee5f32
Exports:allelicRatiocellQCconsensusPartestDispextractResultfeatureQCfusedLassogeneClustermakeForestmakeHeatmapmakeOffByOneAdjMatmakeSimulatedDatamakeStepmakeViolinpreprocesssummaryAllelicRatiowilcoxExt
Dependencies:abindapeglmaskpassbackportsbbmlebdsmatrixbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularCairocatdatacheckmatecirclizecliclueclustercodacodetoolscolorspaceComplexHeatmapcpp11crayoncurlDelayedArrayDelayedMatrixStatsdigestdoParalleldplyrdqrngdynamicTreeCutemdbookfansifarverFNNforeachforestplotformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggbeeswarmggplot2ggrastrggrepelglmnetGlobalOptionsgluegridExtragtablehttrIRangesirlbaisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelpSolvemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmgcvmimemunsellmvtnormnlmenumDerivopensslpbapplypheatmappillarpkgconfigplyrpngR6raggRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppNumericalRcppProgressrjsonrlangRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscuttleshapeSingleCellExperimentsitmosmurfsnowSparseArraysparseMatrixStatsSummarizedExperimentsurvivalsyssystemfontstextshapingtibbletidyselectUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Fit beta-binomial across cell types | allelicRatio |
| Quality control on cells | cellQC |
| Consensus Partitions | consensusPart |
| Estimate overdispersion parameter of a beta-binomial | estDisp |
| Extract results from an airpart analysis | extractResult |
| Quality control on features | featureQC |
| Generalized fused lasso to partition cell types by allelic imbalance | fusedLasso |
| Gene clustering based on allelic ratio matrix with pseudo-count | geneCluster |
| Plot allelic ratio result as forest | makeForest |
| Plot allelic ratio as heatmap | makeHeatmap |
| Generating adjancy matrix for neighboring cell states. | makeOffByOneAdjMat |
| Make simulated data for airpart | makeSimulatedData |
| Plot group partition and posterior allelic ratio estimates by step | makeStep |
| Posterior mean allelic ratio estimates in violin plots | makeViolin |
| Preprocess the SingleCellExperiment | preprocess |
| Allelic ratio summary | summaryAllelicRatio |
| Extension on Pairwise Mann Whitney Wilcoxon Test for partitioning | wilcoxExt |