{"id":24529921,"url":"https://github.com/christianholland/thesis","last_synced_at":"2025-03-15T18:21:00.816Z","repository":{"id":45320607,"uuid":"262848772","full_name":"christianholland/thesis","owner":"christianholland","description":"My PhD thesis","archived":false,"fork":false,"pushed_at":"2022-07-11T15:36:02.000Z","size":42486,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-22T07:52:57.311Z","etag":null,"topics":["bookdown","phd","r","thesis"],"latest_commit_sha":null,"homepage":"https://christianholland-thesis.netlify.app","language":"TeX","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/christianholland.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null}},"created_at":"2020-05-10T18:20:10.000Z","updated_at":"2022-01-09T21:36:11.000Z","dependencies_parsed_at":"2022-09-01T20:22:30.942Z","dependency_job_id":null,"html_url":"https://github.com/christianholland/thesis","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/christianholland%2Fthesis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/christianholland%2Fthesis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/christianholland%2Fthesis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/christianholland%2Fthesis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/christianholland","download_url":"https://codeload.github.com/christianholland/thesis/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243770839,"owners_count":20345356,"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":["bookdown","phd","r","thesis"],"created_at":"2025-01-22T07:53:05.176Z","updated_at":"2025-03-15T18:21:00.794Z","avatar_url":"https://github.com/christianholland.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\"\n)\n```\n\n# My PhD thesis\n\n\u003c!-- badges: start --\u003e\n[![Netlify Status](https://api.netlify.com/api/v1/badges/a71856c3-c83a-4be6-aa3b-642e0e3ec82e/deploy-status)](https://app.netlify.com/sites/christianholland-thesis/deploys)\n\u003c!-- badges: end --\u003e\n\n## From gene expression to pathway and transcription factor activities to study chronic liver diseases\n\nThis thesis is based on three manuscripts each forming a separate chapter. An online version of this thesis can be accessed at [Netlify](https://christianholland-thesis.netlify.app).\n\n### Chapter 1\n\nTransfer of regulatory knowledge from human to mouse for functional genomics analysis ([Publication](https://doi.org/10.1016/j.bbagrm.2019.194431), [GitHub repository](https://github.com/saezlab/ConservedFootprints)).\n\n### Chapter 2\n\nRobustness and applicability of transcription factor and pathway analysis tools \non single-cell RNA-seq data ([Publication](https://doi.org/10.1186/s13059-020-1949-z), [GitHub repository](https://github.com/saezlab/FootprintMethods_on_scRNAseq)).\n\n### Chapter 3\n\nTranscriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and mice ([Publication](https://doi.org/10.1002/hep4.1797), [GitHub repository](https://github.com/saezlab/liver-disease-atlas)).","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchristianholland%2Fthesis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchristianholland%2Fthesis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchristianholland%2Fthesis/lists"}