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
scDD_1.31.0.zip(r-4.5)scDD_1.31.0.zip(r-4.4)scDD_1.31.0.zip(r-4.3)
scDD_1.31.0.tgz(r-4.5-any)scDD_1.31.0.tgz(r-4.4-any)scDD_1.31.0.tgz(r-4.3-any)
scDD_1.31.0.tar.gz(r-4.5-noble)scDD_1.31.0.tar.gz(r-4.4-noble)
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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 4 months agofrom:11f58e6db7. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 29 2025 |
| R-4.5-win | NOTE | Jan 29 2025 |
| R-4.5-mac | WARNING | Jan 29 2025 |
| R-4.5-linux | NOTE | Jan 29 2025 |
| R-4.4-win | NOTE | Jan 29 2025 |
| R-4.4-mac | NOTE | Jan 29 2025 |
| R-4.3-win | NOTE | Jan 29 2025 |
| R-4.3-mac | NOTE | Jan 29 2025 |
Exports:preprocessresultsscDDsideViolinsimulateSettestKS
Dependencies:abindarmaskpassassortheadbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblockmodelingblusterbootbriocallrcaToolscliclustercodacodetoolscolorspacecpp11crayoncurlDelayedArraydescdiffobjdigestdotCall64dqrngEBSeqedgeRevaluatefansifarverfieldsformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshttrigraphIRangesirlbaisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmalme4locfitmagrittrmapsMASSMatrixMatrixGenericsmatrixStatsmclustmetapodmgcvmimeminqamunsellnlmenloptropenssloutlierspillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangrprojrootrsvdS4ArraysS4VectorsScaledMatrixscalesscranscuttleSingleCellExperimentsitmosnowspamSparseArraystatmodSummarizedExperimentsystestthattibbleUCSC.utilsutf8vctrsviridisLitewaldowithrXVector
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 |
