Package: bnem 1.15.0
Martin Pirkl
bnem: Training of logical models from indirect measurements of perturbation experiments
bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate).
Authors:
bnem_1.15.0.tar.gz
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bnem.pdf |bnem.html✨
bnem/json (API)
NEWS
| # Install 'bnem' in R: |
| install.packages('bnem', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/martinfxp/bnem/issues
- bcr - B-Cell receptor signalling perturbations
On BioConductor:bnem-1.15.0(bioc 3.21)bnem-1.14.0(bioc 3.20)
pathwayssystemsbiologynetworkinferencenetworkgeneexpressiongeneregulationpreprocessing
Last updated 5 months agofrom:ea50de29fb. Checks:1 OK, 8 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 27 2025 |
| R-4.5-win | NOTE | Mar 27 2025 |
| R-4.5-mac | NOTE | Mar 27 2025 |
| R-4.5-linux | NOTE | Mar 27 2025 |
| R-4.4-win | NOTE | Mar 27 2025 |
| R-4.4-mac | NOTE | Mar 27 2025 |
| R-4.4-linux | NOTE | Mar 27 2025 |
| R-4.3-win | NOTE | Mar 27 2025 |
| R-4.3-mac | NOTE | Mar 27 2025 |
Exports:absorptionabsorptionIIaddNoisebnembnemBscomputeFcconvertGraphdummyCNOlistepiNEM2BgfindResidualsprocessDataBCRrandomDnfreduceGraphscoreDnfsimBoolGtnsimulateStatesRecursivetransClosetransRedvalidateGraph
Dependencies:abindaffyaffyioamapannotateAnnotationDbiapclusteraskpassbase64encbdsmatrixBHbinomBiobaseBiocGenericsBiocManagerBiocParallelBiostringsbitbit64bitopsblobBoolNetBoutrosLab.plotting.generalbslibcachemCellNOptRclasscliclueclustercodetoolscolorspacecorpcorcpp11crayoncurldata.tableDBIdeldirDEoptimRdigestdipteste1071edgeRellipseepiNEMevaluatefansifarverfastclusterfastICAfastmapflexclustflexmixfontawesomeformatRfpcfsfutile.loggerfutile.optionsgdatagenefiltergenericsGenomeInfoDbGenomeInfoDbDataggdendroggmggplot2gluegmodelsgraphgridExtragtablegtoolshexbinhighrhtmltoolshttrigraphinfotheointerpIRangesisobandjpegjquerylibjsonliteKEGGRESTkernlabknitrlabelinglambda.rlatex2explatticelatticeExtralifecyclelimmaLinnormlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimeminetmnemmodeltoolsmunsellnaturalsortnlmennetopensslpcalgpermutepillarpkgconfigplogrpngprabcluspreprocessCoreproxyR6rappdirsRBGLRColorBrewerRcppRcppArmadilloRcppEigenRCurlRgraphvizrlangrmarkdownrobustbaseRSQLiteRtsneS4VectorssassscalessfsmiscsnowsnowfallstatmodstringistringrsurvivalsvasystibbletinytextsneUCSC.utilsutf8vcdvctrsveganviridisLitevsnwesandersonwithrxfunXMLxtableXVectoryamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Absorption | absorption |
| Inverse absorption | absorptionII |
| Add noise | addNoise |
| B-Cell receptor signalling perturbations | bcr |
| Boolean Nested Effects Model main function | bnem |
| Bootstraped Network | bnemBs |
| Compute differential effects | computeFc |
| Convert normal form | convertGraph |
| Create dummy CNOlist | dummyCNOlist |
| Switch between epiNEM and B-NEM | epiNEM2Bg |
| Compute residuals | findResiduals |
| plot bnem opbject | plot.bnem |
| Plot Bootstrap result | plot.bnemBs |
| plot simulation object | plot.bnemsim |
| BCR perturbation reproduction | processDataBCR |
| sample normal form | randomDnf |
| Reduce graph | reduceGraph |
| score a boolean network | scoreDnf |
| Sample random network and simulate data | simBoolGtn |
| Simulate states | simulateStatesRecursive |
| transitive closure | transClose |
| transitive reduction | transRed |
| validate graph | validateGraph |
