Package: CARNIVAL 2.23.0

Attila Gabor

CARNIVAL: A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs' weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.

Authors:Enio Gjerga [aut], Panuwat Trairatphisan [aut], Anika Liu [ctb], Alberto Valdeolivas [ctb], Nikolas Peschke [ctb], Aurelien Dugourd [ctb], Attila Gabor [cre], Olga Ivanova [aut]

CARNIVAL_2.23.0.tar.gz
CARNIVAL_2.23.0.zip(r-4.7)CARNIVAL_2.23.0.zip(r-4.6)CARNIVAL_2.23.0.zip(r-4.5)
CARNIVAL_2.23.0.tgz(r-4.6-any)CARNIVAL_2.23.0.tgz(r-4.5-any)
CARNIVAL_2.23.0.tar.gz(r-4.7-any)CARNIVAL_2.23.0.tar.gz(r-4.6-any)
CARNIVAL_2.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CARNIVAL/json (API)

# Install 'CARNIVAL' in R:

install.packages('CARNIVAL', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/saezlab/carnival/issues

On BioConductor:CARNIVAL-2.23.0(bioc 3.24)CARNIVAL-2.22.0(bioc 3.23)

transcriptomics geneexpression network causal-models footprints integer-linear-programming pathway-enrichment-analysis

9.50 score 62 stars 2 packages 121 scripts 569 downloads 7 mentions 16 exports 56 dependencies

Last updated from:19f1f66721. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	172
linux-devel-x86_64	NOTE	211
source / vignettes	OK	184
linux-release-x86_64	NOTE	293
macos-release-arm64	NOTE	111
macos-oldrel-arm64	NOTE	105
windows-devel	NOTE	112
windows-release	NOTE	108
windows-oldrel	NOTE	93
wasm-release	OK	125

Exports:checkOptionsValidity defaultCbcSolveCarnivalOptions defaultCplexCarnivalOptions defaultCplexSpecificOptions defaultLpSolveCarnivalOptions generateLpFileCarnival getOptionsList getSupportedSolvers isInputValidCarnival runCARNIVAL runFromLpCarnival runInverseCarnival runVanillaCarnival setCarnivalOptions suggestedCbcSpecificOptions suggestedCplexSpecificOptions

Dependencies:base64enc bit bit64 bslib cachem cli clipr cpp11 crayon digest dplyr evaluate fastmap fontawesome fs generics glue highr hms htmltools igraph jquerylib jsonlite knitr lattice lifecycle lpSolve magrittr Matrix memoise mime pillar pkgconfig prettyunits progress purrr R6 rappdirs readr rjson rlang rmarkdown sass stringi stringr tibble tidyr tidyselect tinytex tzdb utf8 vctrs vroom withr xfun yaml

Contextualizing large scale signalling networks from expression footprints with CARNIVAL

Rendered fromCARNIVAL.Rmdusingknitr::rmarkdown

Last update: 2022-03-09
Started: 2020-04-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Checks if provided option names are valid.	checkOptionsValidity
Sets default CARNIVAL options for cbc.	defaultCbcSolveCarnivalOptions
Sets default CARNIVAL options for cplex.	defaultCplexCarnivalOptions
Sets default options from cplex documentation.	defaultCplexSpecificOptions
Sets default CARNIVAL options for lpSolve.	defaultLpSolveCarnivalOptions
'generateLpFileCarnival'	generateLpFileCarnival
Returns the list of options needed/supported for each solver.	getOptionsList
Returns the list of supported solvers.	getSupportedSolvers
Checks validity of all inputs of CARNIVAL	isInputValidCarnival
Parses the cplex log file and reads some basic information.	parseCplexLog
'runCARNIVAL'	runCARNIVAL
'runCarnivalFromLp'	runFromLpCarnival
'runInverseCarnival'	runInverseCarnival
'runVanillaCarnival'	runVanillaCarnival
Sets CARNIVAL options for the solver.	setCarnivalOptions
Suggests cbc specific options.	suggestedCbcSpecificOptions
Suggests cplex specific options.s	suggestedCplexSpecificOptions
writeCplexCommandFileFromJson	writeCplexCommandFileFromJson