{"id":34512343,"url":"https://github.com/wejlab/tbsignatureprofiler","last_synced_at":"2026-03-12T08:37:18.552Z","repository":{"id":43834679,"uuid":"146775994","full_name":"wejlab/TBSignatureProfiler","owner":"wejlab","description":"Profile RNA-seq data using published TB gene signatures","archived":false,"fork":false,"pushed_at":"2025-09-24T14:58:10.000Z","size":16392,"stargazers_count":12,"open_issues_count":0,"forks_count":13,"subscribers_count":2,"default_branch":"devel","last_synced_at":"2025-09-24T16:42:04.477Z","etag":null,"topics":["bioconductor-package","biomarkers","gene-signatures","tuberculosis"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/wejlab.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","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":"2018-08-30T16:19:47.000Z","updated_at":"2025-09-24T14:58:14.000Z","dependencies_parsed_at":"2024-10-26T03:29:03.903Z","dependency_job_id":"45d35cd9-5fef-42d4-951b-4421ad177a4a","html_url":"https://github.com/wejlab/TBSignatureProfiler","commit_stats":null,"previous_names":["wejlab/tbsignatureprofiler","compbiomed/tbsignatureprofiler"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/wejlab/TBSignatureProfiler","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wejlab%2FTBSignatureProfiler","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wejlab%2FTBSignatureProfiler/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wejlab%2FTBSignatureProfiler/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wejlab%2FTBSignatureProfiler/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/wejlab","download_url":"https://codeload.github.com/wejlab/TBSignatureProfiler/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wejlab%2FTBSignatureProfiler/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":27994412,"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","status":"online","status_checked_at":"2025-12-24T02:00:07.193Z","response_time":83,"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":["bioconductor-package","biomarkers","gene-signatures","tuberculosis"],"created_at":"2025-12-24T04:10:12.164Z","updated_at":"2025-12-24T04:10:14.243Z","avatar_url":"https://github.com/wejlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"## TBSignatureProfiler \u003cimg src=\"https://github.com/wejlab/TBSignatureProfiler-docs/blob/master/lungs1.png?raw=true\" align=\"right\" width=\"170\" /\u003e\n\n[![](https://img.shields.io/badge/bioconductor-3.21-blue)](http://www.bioconductor.org/packages/release/bioc/html/TBSignatureProfiler.html)\n[![codecov](https://codecov.io/gh/wejlab/TBSignatureProfiler/branch/master/graph/badge.svg)](https://codecov.io/gh/wejlab/TBSignatureProfiler)\n[![build](http://www.bioconductor.org/shields/build/devel/bioc/TBSignatureProfiler.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/TBSignatureProfiler/)\n\n## What is the TBSignatureProfiler?\nThe TBSignatureProfiler (TBSP) is an easy-to-use R package for analysis of RNA-seq data using gene signatures for tuberculosis disease presence, risk, progression, treatment failure, and other states. In-package signature profiling is available using common gene set enrichment tools that include GSVA, singscore, and ssGSEA.\n\nUsers can analyze RNA-seq data across 70+ published gene signatures to compare signature performance with clear visualizations (e.g., heatmaps and ROC plots), specificity/sensitivity estimates for predicting binary variables, and cross-validated logistic regression.\n\nThe TBSP can be used as a standalone software package. Data exploration is also available with the accompanying interactive R Shiny application. The R Shiny app is currently functional but more limited in its capabilities than the command line form of the package.\n\n## Documentation\n\nPlease check our website at https://wejlab.github.io/TBSignatureProfiler-docs/.\n\n## Citation\n\nWe used the TBSP to compare 45 gene signatures and differentiate active TB from LTBI in malnourished individuals from India. You can read our paper here: [“Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler”](\nhttps://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-020-05598-z)\n\nPlease cite:\n\n**Johnson, W.E., Odom, A., Cintron, C. et al. Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler. BMC Infect Dis 21, 106 (2021).**\n\n## Installation\n\nThe TBSignatureProfiler requires R Version 4.2.\n\n* Install the development version of the package from Github:\n\n``` r\nif (!requireNamespace(\"devtools\", quietly = TRUE))\n  install.packages(\"devtools\")\ndevtools::install_github(\"wejlab/TBSignatureProfiler\")\n```\n\n* Install the release version of the package from Bioconductor:\n\n``` r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n  install.packages(\"BiocManager\")\nBiocManager::install(\"TBSignatureProfiler\")\n\n```\n\n* Run the TBSP R Shiny app!\n``` r\nlibrary(TBSignatureProfiler)\nTBSPapp()\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwejlab%2Ftbsignatureprofiler","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwejlab%2Ftbsignatureprofiler","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwejlab%2Ftbsignatureprofiler/lists"}