{"id":16320092,"url":"https://github.com/helenalc/msc-thesis","last_synced_at":"2025-05-14T07:12:33.409Z","repository":{"id":105098863,"uuid":"144719727","full_name":"HelenaLC/MSc-thesis","owner":"HelenaLC","description":null,"archived":false,"fork":false,"pushed_at":"2018-08-30T17:49:35.000Z","size":13243,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-02-17T01:29:44.763Z","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/HelenaLC.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":"2018-08-14T12:51:26.000Z","updated_at":"2018-08-30T17:50:26.000Z","dependencies_parsed_at":null,"dependency_job_id":"1e4097d4-8e50-4d57-a527-c784e605a3cb","html_url":"https://github.com/HelenaLC/MSc-thesis","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/HelenaLC%2FMSc-thesis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FMSc-thesis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FMSc-thesis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FMSc-thesis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/HelenaLC","download_url":"https://codeload.github.com/HelenaLC/MSc-thesis/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254092836,"owners_count":22013294,"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":"2024-10-10T22:29:04.253Z","updated_at":"2025-05-14T07:12:28.398Z","avatar_url":"https://github.com/HelenaLC.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MSc thesis on \"Differential Analysis of scRNA-seq data with complex experimental designs\"\n\n### contents\n\n- **scripts:** R code to reproduce all analyses \u0026 figures.\n- **results:** Figures \u0026 data produced by scripts.\n\n### packages\n\n- **pkg:** R package containing method wrappers and utilities for plotting \u0026 evaluation.\n- **fda:** `FDA` package fork w/ modified code of `tperm.fd()` to decrease runtime.\n- **scDD:** `scDD` package fork w/ modified version of `simulateSet()` to prevent repeated running of `findIndex()` \u0026 make simulated counts non-continuous.\n\n### scripts\n\n- **dd_patterns.R**: \u003cbr/\u003e\n    Generates a schematic of differential distribution patterns \u003cbr/\u003e\n    (reproduces: *dd_patterns*)\n    \n- **ECDFs.R**: \u003cbr/\u003e\n    Generates an exemplary set of ECDFs for a 3 vs. 3 sample comparison. \u003cbr/\u003e\n    (reproduces: *ECDFs*)\n    \n- **scDD-sim_ex.R**: \u003cbr/\u003e\n    Visualises an exemplary `scDD` simulation \u003cbr/\u003e\n    (reproduces: *scDD_sim_ex-med_exprs*, *scDD_sim_ex-expr_profiles*)\n  \n- **simDD-seurat.R** \u003cbr/\u003e\n    Evaluates `Seurat` clustering performance on \n    10 simulation replicates w/ randomised parameters \u003cbr/\u003e\n    (reproduces: *simDD-seurat_scores*)\n \n- **simDD-sim_qc.R**: \u003cbr/\u003e\n    Generates basic quality control plots for `simDD` simulated data\n    and data from Koh et al. \u003cbr/\u003e\n    (reproduces: *qc_var_explained*, *qc_lib_sizes*, \n        *qc_top_expr*, *qc_expr_freq_vs_mean*, *qc_disp_vs_mean*)\n        \n- **scDD-null_sim.R**: \u003cbr/\u003e\n    Evaluates method performances on 3 replicates of a null simulation \u003cbr/\u003e\n    (reproduces: *scDD_null_sim*)\n  \n- **diffcyt_runmodes.R**: \u003cbr/\u003e\n    Evaluates the performance of `diffcyt` for varying data inputs \u0026 summary statistics \u003cbr/\u003e\n    (reproduces: *diffcyt_runmodes*)\n\n- **kang-data_prep.R**: \u003cbr/\u003e\n    Performed `Seurat` preprocessing \u0026 constructs a `daFrame` from\n    the Kang et al. raw data available at accession # GSE96583\n  \n- **kang-data_overview.R**: \u003cbr/\u003e\n    Generates general data overview plot for the Kang et al. data set \u003cbr/\u003e\n    (reproduces: *kang_cluster_props*, *kang_tsne*, *kang_nb_cells*)\n\n- **kang-DS_analysis.R**: \u003cbr/\u003e\n    Performs differential analysis using `diffcyt` \u0026 `edgeR` methods\n    \u0026 compares obtained results with thouse published\n    (reproduces: *kang_nb_de_gs*, *kang_overlap*, *kang_pvals*, \n        *kang_top_undetected*, *kang_highest_pvals_xxx*)\n\n- **runtimes-nb_gs.R**: \u003cbr/\u003e\n    Measures method runtimes for increasing numbers of genes\n    (reproduces: *runtimes*)\n    \n- **runtimes-FDA_reso.R**, **runtimes-FDA_nperm.R**: \u003cbr/\u003e\n    Measure `FDA` runtimes for increasing `reso` and `n_perm` parameters\n    (reproduces: *runtimes_FDA_reso/nperm*)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhelenalc%2Fmsc-thesis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhelenalc%2Fmsc-thesis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhelenalc%2Fmsc-thesis/lists"}