Package: scDD 1.31.0
Keegan Korthauer
scDD: Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.
Authors:
scDD_1.31.0.tar.gz
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scDD_1.31.0.tgz(r-4.4-any)scDD_1.31.0.tgz(r-4.3-any)
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scDD.pdf |scDD.html✨
scDD/json (API)
NEWS
| # Install 'scDD' in R: |
| install.packages('scDD', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kdkorthauer/scdd/issues
- scDatEx - Data: Toy example data
- scDatExList - Data: Toy example data list
- scDatExSim - Data: Toy example of simulated data
On BioConductor:scDD-1.31.0(bioc 3.21)scDD-1.30.0(bioc 3.20)
immunooncologybayesianclusteringrnaseqsinglecellmultiplecomparisonvisualizationdifferentialexpression
Last updated 20 days agofrom:11f58e6db7. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:preprocessresultsscDDsideViolinsimulateSettestKS
Dependencies:abindarmaskpassassortheadbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblockmodelingblusterbootbriocallrcaToolscliclustercodacodetoolscolorspacecpp11crayoncurlDelayedArraydescdiffobjdigestdotCall64dqrngEBSeqedgeRevaluatefansifarverfieldsformatRfsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshttrigraphIRangesirlbaisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmalme4locfitmagrittrmapsMASSMatrixMatrixGenericsmatrixStatsmclustmetapodmgcvmimeminqamunsellnlmenloptropenssloutlierspillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR6RColorBrewerRcppRcppEigenrematch2rlangrprojrootrsvdS4ArraysS4VectorsScaledMatrixscalesscranscuttleSingleCellExperimentsitmosnowspamSparseArraystatmodSummarizedExperimentsystestthattibbleUCSC.utilsutf8vctrsviridisLitewaldowithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| calcMV | calcMV |
| calcRP | calcRP |
| classifyDD | classifyDD |
| feDP | feDP |
| findFC | findFC |
| findIndex | findIndex |
| findOutliers | findOutliers |
| getPosteriorParams | getPosteriorParams |
| jointPosterior | jointPosterior |
| lu | lu |
| luOutlier | luOutlier |
| mclustRestricted | mclustRestricted |
| permMclust | permMclust |
| permMclustCov | permMclustCov |
| permMclustGene | permMclustGene |
| permZero | permZero |
| preprocess | preprocess |
| results | results |
| Data: Toy example data | scDatEx |
| Data: Toy example data list | scDatExList |
| Data: Toy example of simulated data | scDatExSim |
| scDD | scDD |
| sideHist | sideHist |
| sideViolin | sideViolin |
| simuDB | simuDB |
| simuDE | simuDE |
| simuDM | simuDM |
| simuDP | simuDP |
| simulateSet | simulateSet |
| singleCellSimu | singleCellSimu |
| testKS | testKS |
| testZeroes | testZeroes |
| validation | validation |
