Package: bnem 1.21.0

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:Martin Pirkl [aut, cre]

bnem_1.21.0.tar.gz
bnem_1.21.0.zip(r-4.7)bnem_1.21.0.zip(r-4.6)bnem_1.21.0.zip(r-4.5)
bnem_1.21.0.tgz(r-4.6-any)bnem_1.21.0.tgz(r-4.5-any)
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bnem_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bnem/json (API)

# 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

Datasets:

bcr - B-Cell receptor signalling perturbations

On BioConductor:bnem-1.21.0(bioc 3.24)bnem-1.20.0(bioc 3.23)

pathways systemsbiology networkinference network geneexpression generegulation preprocessing

4.60 score 2 stars 5 scripts 19 exports 162 dependencies

Last updated from:8c4f4c2c40. Checks:1 FAILURE, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	FAILURE	382
linux-devel-x86_64	NOTE	375
source / vignettes	OK	447
linux-release-x86_64	NOTE	432
macos-release-arm64	NOTE	190
macos-oldrel-arm64	NOTE	349
windows-devel	NOTE	313
windows-release	NOTE	288
windows-oldrel	NOTE	261
wasm-release	OK	216

Exports:absorption absorptionII addNoise bnem bnemBs computeFc convertGraph dummyCNOlist epiNEM2Bg findResiduals processDataBCR randomDnf reduceGraph scoreDnf simBoolGtn simulateStatesRecursive transClose transRed validateGraph

Dependencies:abind affy affyio amap annotate AnnotationDbi apcluster askpass base64enc bdsmatrix BH binom Biobase BiocGenerics BiocManager BiocParallel Biostrings bit bit64 bitops blob BoolNet BoutrosLab.plotting.general bslib cachem CellNOptR class cli clue cluster codetools colorspace corpcor cpp11 crayon curl data.table DBI deldir DEoptimR digest diptest e1071 edgeR ellipse epiNEM evaluate farver fastcluster fastICA fastmap flexclust flexmix fontawesome formatR fpc fs futile.logger futile.options gdata genefilter generics ggdendro ggm ggplot2 glue gmodels graph gridExtra gtable gtools hexbin highr htmltools httr igraph infotheo interp IRanges isoband jpeg jquerylib jsonlite KEGGREST kernlab knitr labeling lambda.r latex2exp lattice latticeExtra lifecycle limma Linnorm lmtest locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mgcv mime minet mnem modeltools naturalsort nlme nnet openssl pcalg permute pkgconfig png prabclus preprocessCore proxy R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rgraphviz rlang rmarkdown robustbase RSQLite Rtsne S4Vectors S7 sass scales Seqinfo sfsmisc snow snowfall statmod stringi stringr survival sva sys tinytex tsne vcd vctrs vegan viridisLite vsn wesanderson withr xfun XML xtable XVector yaml zoo

| Boolean Nested Effects Models: | Inferring the logical signalling of pathways from indirect measurements and biological perturbations.

Rendered frombnem.rmdusingknitr::rmarkdown

Last update: 2020-12-08
Started: 2019-07-12

Citation

Development and contributors

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