Package: CARNIVAL 2.17.0

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]

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CARNIVAL.pdf |CARNIVAL.html✨
CARNIVAL/json (API)
NEWS

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

Peer review:

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

On BioConductor:CARNIVAL-2.17.0(bioc 3.21)CARNIVAL-2.16.0(bioc 3.20)

transcriptomicsgeneexpressionnetworkcausal-modelsfootprintsinteger-linear-programmingpathway-enrichment-analysis

9.03 score 57 stars 1 packages 89 scripts 270 downloads 7 mentions 16 exports 57 dependencies

Last updated 2 months agofrom:153557fd4a. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:checkOptionsValiditydefaultCbcSolveCarnivalOptionsdefaultCplexCarnivalOptionsdefaultCplexSpecificOptionsdefaultLpSolveCarnivalOptionsgenerateLpFileCarnivalgetOptionsListgetSupportedSolversisInputValidCarnivalrunCARNIVALrunFromLpCarnivalrunInverseCarnivalrunVanillaCarnivalsetCarnivalOptionssuggestedCbcSpecificOptionssuggestedCplexSpecificOptions

Dependencies:base64encbitbit64bslibcachemclicliprcpp11crayondigestdplyrevaluatefansifastmapfontawesomefsgenericsgluehighrhmshtmltoolsigraphjquerylibjsonliteknitrlatticelifecyclelpSolvemagrittrMatrixmemoisemimepillarpkgconfigprettyunitsprogresspurrrR6rappdirsreadrrjsonrlangrmarkdownsassstringistringrtibbletidyrtidyselecttinytextzdbutf8vctrsvroomwithrxfunyaml

Contextualizing large scale signalling networks from expression footprints with CARNIVAL

Enio Gjerga, Matteo Spatuzzi, Olga Ivanova,

Rendered fromCARNIVAL.Rmdusingknitr::rmarkdownon Nov 29 2024.

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