{"id":24528917,"url":"https://github.com/saezlab/greta","last_synced_at":"2025-07-02T00:04:18.163Z","repository":{"id":270346293,"uuid":"505838244","full_name":"saezlab/greta","owner":"saezlab","description":"Benchmark of GRNs using the GRETA pipeline","archived":false,"fork":false,"pushed_at":"2025-03-22T16:10:12.000Z","size":1242,"stargazers_count":24,"open_issues_count":4,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-06-07T20:04:51.914Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","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":"LICENSE","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,"zenodo":null}},"created_at":"2022-06-21T12:41:55.000Z","updated_at":"2025-04-09T11:56:14.000Z","dependencies_parsed_at":null,"dependency_job_id":"f6648796-fda5-4d58-891c-d75fa0c4a4b0","html_url":"https://github.com/saezlab/greta","commit_stats":null,"previous_names":["saezlab/greta"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/saezlab/greta","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fgreta","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fgreta/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fgreta/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fgreta/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/greta/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fgreta/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263052431,"owners_count":23406105,"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","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":"2025-01-22T07:33:59.173Z","updated_at":"2025-07-02T00:04:18.139Z","avatar_url":"https://github.com/saezlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Gene Regulatory nETwork Analysis (GRETA) \u003cimg src=\"https://drive.google.com/uc?id=1DFGeAuSp8w1kDlMaS4zyeXfepKVW14Ym\" align=\"right\" width=\"120\" class=\"no-scaled-link\" alt='GRETA logo' /\u003e\n\n\u003c!-- badges: start --\u003e\n[![GitHub issues](https://img.shields.io/github/issues/saezlab/greta.svg)](https://github.com/saezlab/greta/issues/)\n\u003c!-- badges: end --\u003e\n\nCells regulate their functions through gene expression, driven by a complex interplay of transcription factors and other regulatory mechanisms that together can be modeled as gene regulatory networks (GRNs).\nThe emergence of single-cell multi-omics technologies has driven the development of several methods that integrate transcriptomics and chromatin accessibility data to infer GRNs.\n**Gene Regulatory nETwork Analysis (GRETA)** is a `Snakemake` pipeline that implements state-of-the-art multimodal GRN inference methods. It organizes the steps of these methods into a modular framework, enabling users to infer, compare, and benchmark GRN approaches.\n\n\u003cdiv align=\"center\"\u003e\n   \u003cimg src=\"https://drive.google.com/uc?id=1HpJx1deKivG2DRv3uXp_xLz90R0YfOwU\" alt=\"GRETA graphical abstract\" width=\"500\" style=\"pointer-events: none;\" /\u003e\n\u003c/div\u003e\n\n## Installation\nClone repo:\n```\ngit clone git@github.com:saezlab/greta.git\ncd greta\n```\n\nThen create a new enviroment specific for `Snakemake`:\n```\nmamba create -c conda-forge -c bioconda -n snakemake snakemake\nmamba activate snakemake\n```\n\n## Overview\nDue to the magnitude of datasets and analyses, the repository is organized as a reproducible [Snakemake](https://snakemake.readthedocs.io/en/stable/) pipeline and uses [singularity](https://docs.sylabs.io/guides/3.5/user-guide/introduction.html) images to handle dependencies:\n```\ngreta/\n├── config/\n│   ├── slurm/            # Cluster configuration (assumes Slurm architecture)\n│   ├── config.yaml       # Specifies methods, datasets, and databases\n│   └── prior_cats.json   # Specifies database labels for each dataset\n└── workflow/\n    ├── envs/             # Singularity definition (.def) and image (.sif) files\n    ├── rules/            # Snakemake rules for:\n    │   ├── anl              # analyses\n    │   ├── dbs              # databases\n    │   ├── dts              # datasets\n    │   ├── mth              # methods\n    │   └── plt              # plots\n    ├── scripts/          # Helper scripts for:\n    │   ├── anl              # analyses\n    │   ├── dbs              # databases\n    │   ├── dts              # datasets\n    │   ├── mth              # methods\n    │   └── plt              # plots\n    └── Snakefile         # Main Snakemake file\n```\n\nHere are some lines to generate important intermediate outputs:\n```\n# Downloads and processes a dataset, for example pbmc10k\nsnakemake --profile config/slurm/ dts/pbmc10k/cases/all/mdata.h5mu\n\n# Computes Pando's preprocessing step on the pbmc10k dataset\nsnakemake --profile config/slurm/ dts/pbmc10k/cases/all/runs/pando.pre.h5mu\n\n# Computes GRaNIE's p2g step on Pando's pre\nsnakemake --profile config/slurm/ dts/pbmc10k/cases/all/runs/pando.granie.p2g.csv\n\n# Computes CellOracles's tfb step on GRaNIE's p2g\nsnakemake --profile config/slurm/ dts/pbmc10k/cases/all/runs/pando.granie.celloracle.tfb.csv\n\n# Computes Dictys's mdl step on the previous results\nsnakemake --profile config/slurm/ dts/pbmc10k/cases/all/runs/pando.granie.celloracle.dictys.mdl.csv\n\n# Runs all possible method combinations, baselines and original implementations\nsnakemake --profile config/slurm/ anl/topo/pbmc10k.all.sims_mult.csv\n\n# Downloads and processess all databases\nsnakemake --profile config/slurm/ anl/dbs/stats.csv\n\n# Runs the mechanistic metric forecasting (perturbation) for all method combinations\nsnakemake --profile config/slurm/ anl/metrics/mech/prt/knocktf/pbmc10k.all.scores.csv\n\n# Runs the benchmark for all databases and metrics\nsnakemake --profile config/slurm/ anl/metrics/pbmc10k.all.csv\n```\n\n## How to\n- [add methods](docs/mth.md)\n- [add datasets](docs/dts.md)\n- [add databases](docs/dbs.md)\n\n## Citation\nBadia-i-Mompel et al. Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data. *bioRxiv* (2024) [doi:10.1101/2024.12.20.629764](https://doi.org/10.1101/2024.12.20.629764)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fgreta","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fgreta","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fgreta/lists"}