Package: mnem 1.21.0
Martin Pirkl
mnem: Mixture Nested Effects Models
Mixture Nested Effects Models (mnem) is an extension of Nested Effects Models and allows for the analysis of single cell perturbation data provided by methods like Perturb-Seq (Dixit et al., 2016) or Crop-Seq (Datlinger et al., 2017). In those experiments each of many cells is perturbed by a knock-down of a specific gene, i.e. several cells are perturbed by a knock-down of gene A, several by a knock-down of gene B, ... and so forth. The observed read-out has to be multi-trait and in the case of the Perturb-/Crop-Seq gene are expression profiles for each cell. mnem uses a mixture model to simultaneously cluster the cell population into k clusters and and infer k networks causally linking the perturbed genes for each cluster. The mixture components are inferred via an expectation maximization algorithm.
Authors:
mnem_1.21.0.tar.gz
mnem_1.21.0.zip(r-4.5)mnem_1.21.0.zip(r-4.4)mnem_1.21.0.zip(r-4.3)
mnem_1.21.0.tgz(r-4.4-arm64)mnem_1.21.0.tgz(r-4.4-x86_64)mnem_1.21.0.tgz(r-4.3-arm64)mnem_1.21.0.tgz(r-4.3-x86_64)
mnem_1.21.0.tar.gz(r-4.5-noble)mnem_1.21.0.tar.gz(r-4.4-noble)
mnem_1.21.0.tgz(r-4.4-emscripten)mnem_1.21.0.tgz(r-4.3-emscripten)
mnem.pdf |mnem.html✨
mnem/json (API)
NEWS
| # Install 'mnem' in R: |
| install.packages('mnem', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cbg-ethz/mnem/issues
- app - Processed scRNAseq from pooled CRISPR screens
On BioConductor:mnem-1.21.0(bioc 3.20)mnem-1.20.0(bioc 3.19)
Last updated 21 days agofrom:1044450117
Exports:bootstrapclustNEMcreateAppfitaccfuzzyindexgetAffinitygetIChamSimmnemmnemhmnemkmoreboxplotnemplotConvergenceplotDnfscoreAdjsimDatatransitive.closuretransitive.reduction
Dependencies:amapapclusterBiocGenericsclasscliclustercolorspacecpp11data.tableDEoptimRdipteste1071ellipsefansifarverfastclusterflexclustflexmixfpcgdataggdendroggplot2gluegmodelsgraphgtablegtoolsigraphisobandkernlablabelinglatticelifecyclelimmaLinnormmagrittrMASSMatrixmatrixStatsmclustmgcvmodeltoolsmunsellnaturalsortnlmennetpermutepillarpkgconfigprabclusproxyR6RColorBrewerRcppRcppArmadilloRcppEigenRgraphvizrlangrobustbaseRtsnescalessnowsnowfallstatmodtibbletsneutf8vctrsveganviridisLitewesandersonwithrzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Processed scRNAseq from pooled CRISPR screens | app |
| Bootstrap. | bootstrap |
| Cluster NEM. | clustNEM |
| Creating app data. | createApp |
| Simulation accuracy. | fitacc |
| Calculate fuzzy ground truth. | fuzzyindex |
| Calculate responsibilities. | getAffinity |
| Calculate negative penalized log likelihood. | getIC |
| Accuracy for two phis. | hamSim |
| Mixture NEMs - main function. | mnem |
| Hierarchical mixture. | mnemh |
| Learn the number of components K and optimize the mixture. | mnemk |
| Boxplot with scatter and density options | moreboxplot |
| Implementation of the original NEM | nem |
| Plot bootstrap mnem result. | plot.bootmnem |
| Plot mnem result. | plot.mnem |
| Plot mnem_mcmc result. | plot.mnem_mcmc |
| Plot simulated mixture. | plot.mnem_sim |
| Plot convergence of EM | plotConvergence |
| Plot convergence of EM | plotConvergence.mnem |
| Plot disjunctive normal form. | plotDnf |
| Network score | scoreAdj |
| Simulate data. | simData |
| Transitive closure of a directed acyclic graph (dag) | transitive.closure |
| Transitive reduction | transitive.reduction |
