{"id":19592921,"url":"https://github.com/soedinglab/merlot-scripts","last_synced_at":"2025-07-28T00:09:56.479Z","repository":{"id":94860234,"uuid":"120317501","full_name":"soedinglab/merlot-scripts","owner":"soedinglab","description":"Benchmark and plotting scripts for the MERLoT paper","archived":false,"fork":false,"pushed_at":"2019-05-07T15:39:19.000Z","size":142,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-02-26T14:16:07.012Z","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/soedinglab.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-02-05T14:43:41.000Z","updated_at":"2019-05-07T15:39:20.000Z","dependencies_parsed_at":"2023-04-09T21:32:19.560Z","dependency_job_id":null,"html_url":"https://github.com/soedinglab/merlot-scripts","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/soedinglab/merlot-scripts","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fmerlot-scripts","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fmerlot-scripts/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fmerlot-scripts/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fmerlot-scripts/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/soedinglab","download_url":"https://codeload.github.com/soedinglab/merlot-scripts/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fmerlot-scripts/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267442480,"owners_count":24087806,"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":"2025-07-27T02:00:11.917Z","response_time":82,"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":"2024-11-11T08:37:27.597Z","updated_at":"2025-07-28T00:09:56.427Z","avatar_url":"https://github.com/soedinglab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"## benchmark scripts\n\nA collection of scripts that was used to generate and benchmark the simulations provided with the tool MERLoT. Download the expression matrices and parameter files via the [GWDG FTP server](wwwuser.gwdg.de/~compbiol/merlot/). These will be used as examples for the various scripts.\n\nLet `$scripts` be the directory where `merlot-scripts` is downloaded and `$dir` the directory where the simulations are downloaded and unpacked.\n\nMore details are available as comments in each script.\n\n### benchmarkN_serial.sh\nThe entry point script. Will generate simulations, calculate predictions, and evaluate them. This command (provided line 31 is commented out) will run `destiny`, `SLICER`, `Monocle2` and `MERLoT` on the 100 simulated single bifurcation datasets provided for MERLoT:\n\n`$scripts/benchmarkN_serial.sh $scripts test $dir/benchmark1 20 1`\n\nThis script calls a runner script for each simulation via the [`parallel`](https://www.gnu.org/software/parallel/) utility.\n\n### run_as_one.sh\nThis script will calculate the embeddings - run diffusion maps for `destiny` and DDRTree embeddings for `Monocle2` in various configurations. This is done because the diffusion maps and DDRTree embeddings are used by multiple method flavors further in the pipeline and so it is more efficient to calculate them once. The script will then call the master evaluator script for each dataset.\n\n(includes `run_destiny.R`, `run_monocle.R`)\n\n### timed_benchmarksN.sh\nThis script evaluates the runs of each method. By default, it lets each method run for 60 minutes and terminates them if they need longer.\n\n(includes `benchmark_MERLoT_dest.R`, `benchmark_MERLoT_mon.R`, `benchmark_SLICER.R`, `benchmark_destiny.R`, `benchmark_monocl2.R`, `benchmark_stopped.R`)\n\n### simulating data\nThe repository also includes the scripts needed to run simulations (`run_simN.sh`) in the framework of `benchmarkN_serial.sh`. In particular, the parameters for the actual simulations are set in `generate_simN.py`.\n\n### benchmark evaluation \u0026 plotting\nThe repository also includes two collections of scripts that were used to read and evaluate the output of the benchmark. These continue the evaluation indices used in the paper (F1 Measure, Jaccard Index, Matthews Correlation Coefficient, adjusted Mutual Information, Goodman-Kruskall Index) as well as others (`evaluate_method.R`, `various.R`).\n\n## Dependencies\n\nThe following R packages are required:\n\nFrom CRAN:\n\n- `infotheo`\n- `igraph`\n- `entropy`\n- `optparse`\n- `FNN`\n- `viridis`\n- `ggplot2`\n- `ggnetwork`\n- `ggrepel`\n- `network`\n- `intergraph`\n- `mclust`\n- `pdist`\n- `hashmap`\n- `reshape2`\n- `plotly`\n\nFrom Bioconductor:\n\n- `destiny`\n- `monocle`, version 2.7\n- `AnnotationDbi`\n- `org.Mm.eg.db`\n- `org.Hs.eg.db`\n- `topGO`\n\nOther:\n- [`rprosstt`](https://github.com/soedinglab/prosstt-r)\n- [`merlot`](https://github.com/soedinglab/merlot)\n- `slingshot`\n- `ElPiGraph.R`\n- `TSCAN`\n- `SLICER`\n\nPython dependencies:\n\n- `numpy`\n- `scipy`\n- `pandas`\n- `sklearn`\n- \n\n- `prosstt`","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsoedinglab%2Fmerlot-scripts","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsoedinglab%2Fmerlot-scripts","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsoedinglab%2Fmerlot-scripts/lists"}