{"id":21561075,"url":"https://github.com/bmascat/lfq-proteomics-pipeline","last_synced_at":"2025-03-18T04:30:11.385Z","repository":{"id":131664924,"uuid":"289690087","full_name":"bmascat/lfq-proteomics-pipeline","owner":"bmascat","description":"All code, bash scrypts and pipelines used to analyse and visualise proteomic data from my experiments with my first Crispr KO model.","archived":false,"fork":false,"pushed_at":"2022-08-21T13:30:30.000Z","size":43,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-24T11:23:43.228Z","etag":null,"topics":["bioinformatics","goterm","over-representation-analysis","proteomics","proteomics-data-analysis"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bmascat.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}},"created_at":"2020-08-23T13:19:50.000Z","updated_at":"2024-04-22T11:38:28.000Z","dependencies_parsed_at":null,"dependency_job_id":"785b0598-0e2e-4b19-ad95-8b2bbf9196c3","html_url":"https://github.com/bmascat/lfq-proteomics-pipeline","commit_stats":null,"previous_names":["bmascat/lfq-proteomics-pipeline"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bmascat%2Flfq-proteomics-pipeline","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bmascat%2Flfq-proteomics-pipeline/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bmascat%2Flfq-proteomics-pipeline/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bmascat%2Flfq-proteomics-pipeline/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bmascat","download_url":"https://codeload.github.com/bmascat/lfq-proteomics-pipeline/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244156337,"owners_count":20407497,"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":["bioinformatics","goterm","over-representation-analysis","proteomics","proteomics-data-analysis"],"created_at":"2024-11-24T09:18:42.530Z","updated_at":"2025-03-18T04:30:11.349Z","avatar_url":"https://github.com/bmascat.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Proteomic analysis of CRISPR Hela KO Alms1 after TGF-B stimulation\n\nAll code and pipelines used to analyze and visualize proteomic data from my experiments with my first Crispr KO model\n\n\u003cp align=\"center\"\u003e\n\u003cimg width=\"680\" alt=\"image\" src=\"https://user-images.githubusercontent.com/43313385/185793045-267fe5a0-4bc1-42bf-9f81-bf1ec2e682fa.png\"\u003e\n\u003c/p\u003e\n\nDifferenticial expression analysis was performed with DEP package:\n\n\u003eZhang X, Smits A, van Tilburg G, Ovaa H, Huber W, Vermeulen M (2018). “Proteome-wide identification of ubiquitin interactions using UbIA-MS.” Nature Protocols, 13, 530–550.\n\nGo-Terms analysis and data results visualizations was performed with Clusterprofiler and GOplot packages to R:\n\n\u003eYu G, Wang L, Han Y, He Q (2012). “clusterProfiler: an R package for comparing biological themes among gene clusters.” OMICS: A Journal of Integrative Biology, 16(5), 284-287. doi: 10.1089/omi.2011.0118.\n\n\u003eWalter, Wencke, Fátima Sánchez-Cabo, and Mercedes Ricote. \"GOplot: an R package for visually combining expression data with functional analysis.\" Bioinformatics (2015): btv300.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbmascat%2Flfq-proteomics-pipeline","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbmascat%2Flfq-proteomics-pipeline","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbmascat%2Flfq-proteomics-pipeline/lists"}