{"id":24528984,"url":"https://github.com/saezlab/carnival-bioconductor-dev","last_synced_at":"2025-10-05T13:38:57.186Z","repository":{"id":77872497,"uuid":"221483854","full_name":"saezlab/CARNIVAL-Bioconductor-Dev","owner":"saezlab","description":"Provisional repository for the development of CARNIVAL package for Bioconductor","archived":false,"fork":false,"pushed_at":"2020-08-25T20:31:17.000Z","size":9703,"stargazers_count":1,"open_issues_count":4,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-15T17:44:36.899Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/saezlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-11-13T14:56:07.000Z","updated_at":"2020-09-14T17:28:26.000Z","dependencies_parsed_at":"2023-03-04T02:45:47.090Z","dependency_job_id":null,"html_url":"https://github.com/saezlab/CARNIVAL-Bioconductor-Dev","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/saezlab/CARNIVAL-Bioconductor-Dev","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCARNIVAL-Bioconductor-Dev","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCARNIVAL-Bioconductor-Dev/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCARNIVAL-Bioconductor-Dev/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCARNIVAL-Bioconductor-Dev/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/CARNIVAL-Bioconductor-Dev/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCARNIVAL-Bioconductor-Dev/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278464314,"owners_count":25991176,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-05T02:00:06.059Z","response_time":54,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-01-22T07:34:17.315Z","updated_at":"2025-10-05T13:38:57.146Z","avatar_url":"https://github.com/saezlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"This repository is outdated and kept mostly for dt and mult_cond functionalities. Merging them to the main CARNIVAL repository might not be as straightforward since code organization in CARNIVAL-Bioconductor-Dev differs from the main CARNIVAL repository.\n\n# CARNIVAL\n\nCARNIVAL is an R-package providing a framework to perform causal reasoning to infer a subset of signalling network from transcriptomics data. This work was originally based on [Melas et al.](https://pubs.rsc.org/en/content/articlehtml/2015/ib/c4ib00294f) with a number improved functionalities comparing to the original version.\nTranscription factors’ (TFs) activities and pathway scores from gene expressions can be inferred with our in-house tools [DoRothEA](https://github.com/saezlab/DoRothEA) \u0026 [PROGENy](https://github.com/saezlab/progeny), respectively.\nTFs’ activities and signed directed protein-protein interaction networks +/- drug targets and pathway scores are then used to derive a series of linear constraints to generate integer linear programming (ILP) problems. \nAn ILP solver (CPLEX) is subsequently applied to identify the sub-network topology with minimised discrepancies on fitting error and model size.\n\nMore detailed descriptions of CARNIVAL, benchmarking and applicational studies can be found on it's dedicated [web-page](https://saezlab.github.io/CARNIVAL/) and in [Liu, Trairatphisan, Gjerga et al.](https://www.nature.com/articles/s41540-019-0118-z):\n\n\u003e Liu A*, Trairatphisan P*, Gjerga E*, Didangelos A, Barratt J, Saez-Rodriguez J. (2019). From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL. *npj Systems Biology and Applications*, https://doi.org/10.1038/s41540-019-0118-z (*equal contributions).\n\n\n## Getting Started\n\nA tutorial for preparing CARNIVAL input files starting from differentially gene expression (DEG) and for running the CARNIVAL pipeline are provided as vignettes in R-Markdown, R-script and HTML formats. The wrapper script \"runCARNIVAL\" was introduced to take input arguments, pre-process input descriptions, run optimisation and export results as network files and figures. Three built-in CARNIVAL examples are also supplied as case studies for users.\n\n### Prerequisites\n\nCARNIVAL requires the interactive version of IBM Cplex or CBC-COIN solver as the network optimiser. The IBM ILOG Cplex is freely available through Academic Initiative [here](https://www.ibm.com/products/ilog-cplex-optimization-studio?S_PKG=CoG\u0026cm_mmc=Search_Google-_-Data+Science_Data+Science-_-WW_IDA-_-+IBM++CPLEX_Broad_CoG\u0026cm_mmca1=000000RE\u0026cm_mmca2=10000668\u0026cm_mmca7=9041989\u0026cm_mmca8=kwd-412296208719\u0026cm_mmca9=_k_Cj0KCQiAr93gBRDSARIsADvHiOpDUEHgUuzu8fJvf3vmO5rI0axgtaleqdmwk6JRPIDeNcIjgIHMhZIaAiwWEALw_wcB_k_\u0026cm_mmca10=267798126431\u0026cm_mmca11=b\u0026mkwid=_k_Cj0KCQiAr93gBRDSARIsADvHiOpDUEHgUuzu8fJvf3vmO5rI0axgtaleqdmwk6JRPIDeNcIjgIHMhZIaAiwWEALw_wcB_k_|470|135655\u0026cvosrc=ppc.google.%2Bibm%20%2Bcplex\u0026cvo_campaign=000000RE\u0026cvo_crid=267798126431\u0026Matchtype=b\u0026gclid=Cj0KCQiAr93gBRDSARIsADvHiOpDUEHgUuzu8fJvf3vmO5rI0axgtaleqdmwk6JRPIDeNcIjgIHMhZIaAiwWEALw_wcB). The [CBC](https://projects.coin-or.org/Cbc) solver is open source and freely available for any user. \n\n### Installing\n\nCARNIVAL is currently available for the installation as an R-package from our GitHub page\n\n```R\n# Install CARNIVAL from Github using devtools\n# install.packages('devtools') # in case devtools hasn't been installed\nlibrary(devtools)\ninstall_github('saezlab/CARNIVAL-Bioconductor-Dev', build_vignettes = TRUE)\n# or download the source file from GitHub and install from source\ninstall.packages('path_to_extracted_CARNIVAL_directory', repos = NULL, type=\"source\")\n```\n\n## Running CARNIVAL\n\nTo obtain the list of tutorials/vignettes of the CARNIVAL package, user can start with typing the following commmand on R-console:\n\n```R\nvignette(\"CARNIVAL-vignette\")\n```\n\n## License\n\nDistributed under the GNU GPLv3 License. See accompanying file [LICENSE.txt](https://github.com/saezlab/CARNIVAL/blob/master/LICENSE.txt) or copy at [http://www.gnu.org/licenses/gpl-3.0.html](http://www.gnu.org/licenses/gpl-3.0.html).\n\n## References\n\n[Melas et al.](https://pubs.rsc.org/en/content/articlehtml/2015/ib/c4ib00294f):\n\n\u003e Melas IN, Sakellaropoulos T, Iorio F, Alexopoulos L, Loh WY, Lauffenburger DA, Saez-Rodriguez J, Bai JPF. (2015). Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury. *Integrative Biology*, Issue 7, Pages 904-920, https://doi.org/10.1039/C4IB00294F.\n\n[DoRothEA v2 - Garcia-Alonso et al.](https://www.biorxiv.org/content/early/2018/06/03/337915):\n\n\u003e Garcia-Alonso L, Ibrahim MM, Turei D, Saez-Rodriguez J. (2018). Benchmark and integration of resources for the estimation of human transcription factor activities. *bioRXiv*, https://doi.org/10.1101/337915.\n\n[PROGENy - Schubert et al.](https://www.nature.com/articles/s41467-017-02391-6):\n\n\u003e Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N, Saez-Rodriguez J. (2018). Perturbation-response genes reveal signaling footprints in cancer gene expression. *Nature Communication*, Issue 9, Nr. 20. https://doi.org/10.1038/s41467-017-02391-6.\n\n\n## Acknowledgement\n\nCARNIVAL has been developed as a computational tool to analyse -omics data within the [TransQST Consortium](https://transqst.org) and [H2020 Symbiosys ITN Training Network](https://www.h2020symbiosys.eu/).\n\n\"This project has received funding by the European Union’s H2020 program (675585 Marie-Curie ITN ‘‘SymBioSys’’) and the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 116030. The Joint Undertaking receives support from the European Union's Horizon 2020 research and innovation programme and EFPIA.\"\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fcarnival-bioconductor-dev","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fcarnival-bioconductor-dev","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fcarnival-bioconductor-dev/lists"}