{"id":39554213,"url":"https://github.com/jackhump/als_spinalcord_qtls","last_synced_at":"2026-01-18T07:00:42.917Z","repository":{"id":185141737,"uuid":"399518518","full_name":"jackhump/ALS_SpinalCord_QTLs","owner":"jackhump","description":"Data Portal for NYGC ALS Spinal Cord","archived":false,"fork":false,"pushed_at":"2023-08-30T17:58:28.000Z","size":24914,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2023-08-31T06:36:00.370Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"HTML","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/jackhump.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}},"created_at":"2021-08-24T15:34:53.000Z","updated_at":"2023-08-31T06:36:00.371Z","dependencies_parsed_at":null,"dependency_job_id":"95f94a10-6590-4a16-b5ba-5341f6a54d8a","html_url":"https://github.com/jackhump/ALS_SpinalCord_QTLs","commit_stats":null,"previous_names":["jackhump/als_spinalcord_qtls"],"tags_count":0,"template":null,"template_full_name":null,"purl":"pkg:github/jackhump/ALS_SpinalCord_QTLs","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jackhump%2FALS_SpinalCord_QTLs","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jackhump%2FALS_SpinalCord_QTLs/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jackhump%2FALS_SpinalCord_QTLs/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jackhump%2FALS_SpinalCord_QTLs/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jackhump","download_url":"https://codeload.github.com/jackhump/ALS_SpinalCord_QTLs/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jackhump%2FALS_SpinalCord_QTLs/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28532579,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-18T00:39:45.795Z","status":"online","status_checked_at":"2026-01-18T02:00:07.578Z","response_time":98,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":"2026-01-18T07:00:24.067Z","updated_at":"2026-01-18T07:00:42.895Z","avatar_url":"https://github.com/jackhump.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"## ALS Spinal Cord differential expression and molecular QTLs\n\nJack Humphrey 2019-2023\n\n![deg figure](https://github.com/jackhump/ALS_SpinalCord_QTLs/raw/master/deg_figure.png)\n\n## Manuscript\n\n[Publication in Nature Neuroscience](https://www.nature.com/articles/s41593-022-01205-3)\n\n[Link to preprint on medrxiv](https://www.medrxiv.org/content/10.1101/2021.08.31.21262682v1)\n\n## Shiny App\n\n[Launch Shiny app](https://rstudio-connect.hpc.mssm.edu/als_spinal_cord_browser/)\n\n[source code](https://github.com/jackhump/ALS_SpinalCord_QTLs/blob/master/als_spinal_cord_browser/app.R)\n\n## Data Availability\n\n[Raw RNA-seq data - Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137810)\n\n[Processed gene expression count matrices with de-identified metadata - Zenodo](https://zenodo.org/record/6385747) \n\n[An HTML vignette on downloading the count data from Zenodo and performing differential expression](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/DE_Vignette.html)\n\nWhole genome sequencing data - dbGAP (in progress). \n\n[Full summary statistics for expression and splicing QTLs - Zenodo](https://zenodo.org/record/5248758).\n\n[All TWAS weight files - Zenodo](https://zenodo.org/record/5256613)\n\n[All marker genes used](https://github.com/jackhump/ALS_SpinalCord_QTLs/tree/master/markers)\n\n## Rmarkdown workbooks written for the project.\n\nWorkbooks are available as [RMarkdown files](https://github.com/jackhump/ALS_SpinalCord_QTLs/tree/master/scripts). Knitted HTMLs can be browsed with the links below.\n\n### Data QC and setup\n\n[RNA-seq QC](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_covariates_setup.html)\n\nWGS QC pipeline hosted [here](https://github.com/jackhump/WGS-QC-Pipeline)\n\n[Building sets of marker genes](https://github.com/jackhump/ALS_SpinalCord_QTLs/blob/master/scripts/ALS_marker_lists.Rmd)\n\nAll marker sets are shared as RData objects [here](https://github.com/jackhump/ALS_SpinalCord_QTLs/tree/master/markers)\n \n### Differential expression\n\n[Running differential expression](https://github.com/jackhump/ALS_SpinalCord_QTLs/blob/master/scripts/ALS_differential_expression.Rmd)\n\n[Volcano plots, GSEA, marker gene overlaps](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_deg_functions.html)\n\n[Cell-type deconvolution](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_deconvolution.html)\n\n### Co-expression networks\n\n[Building co-expression networks, associations with traits and GO](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_WGCNA.html)\n\n### Quantitative Trait Loci (QTLs)\n\n[QTL results per region and sharing with GTEx](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_QTL_results.html)\n\n[Colocalisation with ALS GWAS](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_COLOC.html)\n\n[Transcriptome-wide association study - TWAS](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_TWAS.html)\n\n### Gene prioritisation\n\n[C9orf72 and ATXN3](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ATXN3_C9orf72.html)\n\n[Transcript plots](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_locus_plots.html)\n\n[Localising genes to cell-types](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_genes_celltypes.html)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjackhump%2Fals_spinalcord_qtls","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjackhump%2Fals_spinalcord_qtls","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjackhump%2Fals_spinalcord_qtls/lists"}