{"id":18050234,"url":"https://github.com/csoneson/wagneremt2020","last_synced_at":"2025-04-05T06:21:49.704Z","repository":{"id":79790576,"uuid":"278104846","full_name":"csoneson/WagnerEMT2020","owner":"csoneson","description":null,"archived":false,"fork":false,"pushed_at":"2021-02-04T13:50:34.000Z","size":48,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-10T14:11:22.253Z","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/csoneson.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":"2020-07-08T14:01:18.000Z","updated_at":"2021-03-23T09:55:09.000Z","dependencies_parsed_at":"2023-03-30T20:05:55.928Z","dependency_job_id":null,"html_url":"https://github.com/csoneson/WagnerEMT2020","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csoneson%2FWagnerEMT2020","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csoneson%2FWagnerEMT2020/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csoneson%2FWagnerEMT2020/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csoneson%2FWagnerEMT2020/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/csoneson","download_url":"https://codeload.github.com/csoneson/WagnerEMT2020/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247295886,"owners_count":20915545,"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":"2024-10-30T21:11:00.474Z","updated_at":"2025-04-05T06:21:49.680Z","avatar_url":"https://github.com/csoneson.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Mass Cytometric and Transcriptomic Profiling of Epithelial-Mesenchymal Transitions in Human Mammary Cell Lines\n\nThis repository contains the workflow for analyzing the RNA-seq data in \n\n* Wagner _et al_ (2021): Mass Cytometric and Transcriptomic Profiling of Epithelial-Mesenchymal Transitions in Human Mammary Cell Lines\n\nThe workflow structure is based on [`ARMOR`](https://github.com/csoneson/armor) ([Orjuela, Huang, Hembach _et al_, 2019](https://www.g3journal.org/content/9/7/2089.long)). To run the workflow and regenerate the results, follow the instructions below.\n\n### Preparation\n\n#### Download the data\n\nThe FASTQ files have been uploaded to ArrayExpress, with accession number [E-MTAB-9365](https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9365/). Download the 32 FASTQ files, and place them in a subfolder named `FASTQ`.\n\n#### Download the reference files\n\nThe analysis was performed using the Gencode v34 reference. Download the following files, unzip them, and place them in a subfolder named `reference_files`:\n\n* genome: `ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz`\n* transcriptome: `ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.transcripts.fa.gz`\n* gtf file: `ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz`\n\n#### Run the workflow\n\nTo run the workflow, first make sure that `snakemake` is available. Then, set up the conda environments:\n\n```\nsnakemake --use-conda setup --cores 1\n```\n\nCheck that all inputs are correctly specified:\n\n```\nsnakemake --use-conda checkinputs --cores 1\n```\n\nThen you can run the full workflow as follows:\n\n```\nsnakemake --use-conda --cores 16\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcsoneson%2Fwagneremt2020","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcsoneson%2Fwagneremt2020","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcsoneson%2Fwagneremt2020/lists"}