{"id":38545032,"url":"https://github.com/fertiglab/emt_ewald","last_synced_at":"2026-01-17T07:17:48.209Z","repository":{"id":146065776,"uuid":"389627035","full_name":"FertigLab/EMT_Ewald","owner":"FertigLab","description":"Curated set of analysis scripts for single cell data from the Ewald Lab.","archived":false,"fork":false,"pushed_at":"2022-07-25T15:35:57.000Z","size":2007,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-10-25T14:41:36.675Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/FertigLab.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2021-07-26T12:37:15.000Z","updated_at":"2022-11-05T21:06:56.000Z","dependencies_parsed_at":"2023-06-12T12:00:41.525Z","dependency_job_id":null,"html_url":"https://github.com/FertigLab/EMT_Ewald","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/FertigLab/EMT_Ewald","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FertigLab%2FEMT_Ewald","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FertigLab%2FEMT_Ewald/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FertigLab%2FEMT_Ewald/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FertigLab%2FEMT_Ewald/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/FertigLab","download_url":"https://codeload.github.com/FertigLab/EMT_Ewald/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FertigLab%2FEMT_Ewald/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28503414,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-17T06:57:29.758Z","status":"ssl_error","status_checked_at":"2026-01-17T06:56:03.931Z","response_time":85,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2026-01-17T07:17:48.131Z","updated_at":"2026-01-17T07:17:48.197Z","avatar_url":"https://github.com/FertigLab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# EMT_Ewald\nCurated set of analysis scripts for single cell data from the Ewald Lab.\n\n### 1_CombineData.ipynb\n#### Description - Joins the counts data together\n##### Input \n* D1-D3-D5-byHaiping/D1/filtered_feature_bc_matrix/matrix.mtx\n* D1-D3-D5-byHaiping/D1/filtered_feature_bc_matrix/barcodes.tsv\n* D1-D3-D5-byHaiping/D1/filtered_feature_bc_matrix/features.tsv\n* D1-D3-D5-byHaiping/D3/filtered_feature_bc_matrix/matrix.mtx\n* D1-D3-D5-byHaiping/D3/filtered_feature_bc_matrix/barcodes.tsv\n* D1-D3-D5-byHaiping/D3/filtered_feature_bc_matrix/features.tsv\n* D1-D3-D5-byHaiping/D5/filtered_feature_bc_matrix/matrix.mtx\n* D1-D3-D5-byHaiping/D5/filtered_feature_bc_matrix/barcodes.tsv\n* D1-D3-D5-byHaiping/D5/filtered_feature_bc_matrix/features.tsv\n##### Output\n* mergedAdata.h5ad\n\n### 2_cleanData.ipynb\n#### Description - Preprocesses the combined data\n##### Input \n* mergedAdata.h5ad\n##### Output\n* labelledAdata.h5ad\n* data/dataMatrix.mtx'\n* data/obs.csv\n* data/var.csv\n* rawCleanadata.h5ad\n* data/dataMatrixClean.mtx\n* data/obsClean.csv\n* data/varClean.csv\n\n### 3_ClusteringAfterBatchCorrection.Rmd\n#### Description - Create CDS with the “clean” data. CDS is preprocessed.\n##### Input \n* data/dataMatrixClean.mtx\n* data/obsClean.csv\n* data/varClean.csv\n##### Output\n* intermediateData/cdsBasic.RDS\n* intermediateData/cdsBasic.RDS\n* data/normalizedMatrix.mtx\n* intermediateData/cdsNormalizedDimReduced.rds\n* intermediateData/cdsDayCorrected.RDS\n\n### 4_EJFPreprocessingAnalysis.Rmd\n#### Description - Run pseudotime for matrigel and collagen\n##### Input \n* intermediateData/cdsBasic.RDS\n* geneList.csv\n##### No Output\n\n### 5_EJFPreprocessingAnalysis.R\n#### Description - Run pseudotime for matrigel and collagen\n##### Input \n* cdsBasic.RDS  \n* geneList.csv\n##### Output\n* EJFPsuedotimeResults2Mar2020.Rda\n\n### 6_PseudotimeCorrectedData.Rmd\n#### Description - Process and plot the corrected data\n##### Input \n* intermediateData/cdsDayCorrected.RDS\n* geneList.csv\n##### No Output\n\n### 7_ScanpyEMT.ipynb\n#### Description - Calculate and export cell cycle \n##### Input \n* rawCleanadata.h5ad\n* regev_lab_cellCycle_smouse.txt\n* regev_lab_cellCycle_mmouse.txt\n##### Output\n* obs.csv\n\n### 8_addCellCycle.Rmd\n#### Description - Add cell cycle to cds objects\n##### Input \n* EJFPsuedotimeResults2Mar2020.Rda\n* obs.csv\n##### Output\n* cellCycle_EJFPsuedotimeResults2Mar2020.Rda\n\n### 9_CoGAPSData_collagen.Rmd\n#### Description - Calculate top collagen genes and subset the data to those genes for CoGAPS\n##### Input \n* EJFPsuedotimeResults2Mar2020.Rda\n##### Output\n* sbstCds.rds\n* countsSbstCds.rds\n\n### 10_cogapsObjects_collagen.Rmd\n#### Description - Create CoGAPS objects for the collagen gene subset\n##### Input \n* countsSbstCds.rds\n##### Output\n* emtMat.mtx\n* emtParams.rds\n\n### 11_ewald_gwCogapsAnalysis_collagen.Rmd\n#### Description - Analyze CoGAPS results\n##### Input \n* sbstCds.rds\n* CoGAPS results\n##### Output\n* UMAPS\n* Boxplots\n* patternMarkers_emtGwCogaps_20.csv\n\n### 12_cogapsVisuals_collagen.Rmd\n#### Description - Create heatmap and gene rank file for CoGAPS result\n##### Input \n* gwCogapsRes/emtGwCogaps_20.rds\n* geneList.csv\n##### Output\n* emtGeneRanks.csv\n\n### Ran gene set analysis using MSigDb\n#### Input\n* Pattern marker genes\n#### Output\n* Pathway results\n\n### 13_Figure.Rmd\n#### Description - Create the first set of figures\n##### Input \n* cellCycle_EJFPsuedotimeResults2Mar2020.Rda\n* gwCogapsRes/emtGwCogaps_20.rds\n* msigdb/emtPatterns.csv\n* patternMarkers_emtGwCogaps_20.csv\n* geneList.csv\n* msigdb/emtPatterns.csv\n* emtResults.csv\n##### Output\n* Figures\n\n### 14_ChungProjection.Rmd\n#### Description - Format the Chung single cell data, subset to tumor cells, run ProjectR\n##### Input \n* GSE75688_GEO_processed_Breast_Cancer_raw_TPM_matrix.txt\n* GSE75688_final_sample_information.txt\n* gwCogapsRes/emtGwCogaps_20.rds\n##### Output\n* HumanTumorCoGAPSprojection.rdata\n* Projected pattern umaps\n\n### 15_CoGAPSData_matrigel.Rmd\n#### Description - Subset to top collagen genes for the matrigel data for CoGAPS\n##### Input \n* EJFPsuedotimeResults2Mar2020.Rda\n* emtGwCogaps_20.rds\n##### Output\n* 15_sbstCdsMatrigel.rds\n* 15_countsSbstCdsMatrigel.rds\n\n### 16_cogapsObjects_matrigel.Rmd\n#### Description - Create the cogaps objects for the matrigel cogaps runs\n##### Input \n* 15_countsSbstCdsMatrigel.rds\n##### Output\n* 16_sampleGeneNamesMatrigel.rdata\n* 16_emtMatMatrigel.mtx\n* 16_emtParamsMatrigel.rds\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffertiglab%2Femt_ewald","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffertiglab%2Femt_ewald","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffertiglab%2Femt_ewald/lists"}