Package: scDD 1.37.0

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:Keegan Korthauer [cre, aut]

scDD_1.37.0.tar.gz
scDD_1.37.0.zip(r-4.7)scDD_1.37.0.zip(r-4.6)scDD_1.37.0.zip(r-4.5)
scDD_1.37.0.tgz(r-4.6-any)scDD_1.37.0.tgz(r-4.5-any)
scDD_1.37.0.tar.gz(r-4.7-any)scDD_1.37.0.tar.gz(r-4.6-any)
scDD_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scDD/json (API)

# 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

Datasets:

scDatEx - Data: Toy example data
scDatExList - Data: Toy example data list
scDatExSim - Data: Toy example of simulated data

On BioConductor:scDD-1.37.0(bioc 3.24)scDD-1.36.0(bioc 3.23)

immunooncology bayesian clustering rnaseq singlecell multiplecomparison visualization differentialexpression

8.29 score 35 stars 74 scripts 16 mentions 6 exports 107 dependencies

Last updated from:287a78c1e1. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	219
linux-devel-x86_64	NOTE	438
source / vignettes	OK	315
linux-release-x86_64	NOTE	440
macos-release-arm64	NOTE	318
macos-oldrel-arm64	NOTE	247
windows-devel	NOTE	519
windows-release	NOTE	486
windows-oldrel	NOTE	521
wasm-release	OK	169

Exports:preprocess results scDD sideViolin simulateSet testKS

Dependencies:abind arm assorthead beachmat BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular bitops blockmodeling bluster boot brio callr caTools cli cluster coda codetools cpp11 crayon DelayedArray desc diffobj dotCall64 dqrng EBSeq edgeR evaluate farver fields formatR fs futile.logger futile.options generics GenomicRanges ggplot2 glue gplots gtable gtools igraph IRanges irlba isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle limma lme4 locfit magrittr maps MASS Matrix MatrixGenerics matrixStats mclust metapod minqa nlme nloptr otel outliers pkgbuild pkgconfig pkgload praise processx ps R6 rbibutils RColorBrewer Rcpp RcppEigen Rdpack reformulas rlang rprojroot rsvd S4Arrays S4Vectors S7 ScaledMatrix scales scran scuttle Seqinfo SingleCellExperiment sitmo snow spam SparseArray statmod SummarizedExperiment testthat vctrs viridisLite waldo withr XVector

scDD Quickstart

Rendered fromscDD.Rnwusingknitr::knitr

Last update: 2018-03-23
Started: 2016-12-14

Citation

Development and contributors

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