{"id":22731034,"url":"https://github.com/genentech/isosceles","last_synced_at":"2025-08-25T01:32:41.212Z","repository":{"id":181328090,"uuid":"665751214","full_name":"Genentech/Isosceles","owner":"Genentech","description":"The Isoforms from Single-Cell; Long-read Expression Suite","archived":false,"fork":false,"pushed_at":"2025-01-14T00:20:32.000Z","size":26805,"stargazers_count":25,"open_issues_count":9,"forks_count":1,"subscribers_count":3,"default_branch":"devel","last_synced_at":"2025-03-27T14:48:00.029Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","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/Genentech.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","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":"2023-07-12T23:28:54.000Z","updated_at":"2025-03-13T01:01:41.000Z","dependencies_parsed_at":"2024-12-06T01:22:40.223Z","dependency_job_id":"d4e6ad91-68cf-4004-a01c-032146bf91b7","html_url":"https://github.com/Genentech/Isosceles","commit_stats":null,"previous_names":["timbitz/isosceles","genentech/isosceles"],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/Genentech/Isosceles","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FIsosceles","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FIsosceles/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FIsosceles/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FIsosceles/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Genentech","download_url":"https://codeload.github.com/Genentech/Isosceles/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FIsosceles/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":271991125,"owners_count":24854712,"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":"2025-08-24T02:00:11.135Z","response_time":111,"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":"2024-12-10T19:19:11.363Z","updated_at":"2025-08-25T01:32:41.196Z","avatar_url":"https://github.com/Genentech.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Isosceles \n\nIsosceles (**Iso**forms from **S**ingle-**Ce**ll; **L**ong-read **E**xpression \n**S**uite) is an R package dedicated to transcript detection and quantification \nfrom long reads, supporting both bulk RNA-Seq and scRNA-Seq technologies.\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"docs/Isosceles_header.gif\" width=\"600\"\u003e\n\u003c/p\u003e\n\n\nKabza M., Ritter A., Byrne A., Sereti K., Le D., Stephenson W., Sterne-Weiler T. Accurate long-read transcript discovery and quantification at single-cell, pseudo-bulk and bulk resolution with Isosceles. _Nat Commun_ **15**, 7316 (2024). https://doi.org/10.1038/s41467-024-51584-3\n\n## Installation\n\nIsosceles can be installed using the following commands:\n```r\ninstall.packages(c(\"BiocManager\", \"devtools\"))\nBiocManager::install(c(\"scran\", \"scater\", \"uwot\", \"dittoSeq\", \"DEXSeq\", \n                       \"Nebulosa\", \"ggbio\", \"BiocStyle\"))\ndevtools::install_github(\"Genentech/Isosceles\", dependencies = TRUE, upgrade = TRUE,\n                         INSTALL_opts = \"--install-tests\")\n```\n\nWe found that some versions of Isosceles' dependencies don't work together well, \nwhich might cause problems with testing the package or building the vignettes. \nIf you encounter such issues, re-installing certain packages might be helpful: \n```r\ninstall.packages(\"irlba\") \ndevtools::install_github(\"powellgenomicslab/Nebulosa\", upgrade = FALSE) \n```\n\nLoad the Isosceles package:\n```r\nlibrary(Isosceles)\n```\n\n## Usage\n\nYou can follow along with our vignettes ([Introduction to the Isosceles package](https://genentech.github.io/Isosceles/docs/Isosceles.html), [Mouse E18 brain data analysis](https://genentech.github.io/Isosceles/docs/Mouse_E18_brain_analysis.html))\nor the [reference manual](https://github.com/Genentech/Isosceles/blob/devel/docs/Isosceles.pdf)!\n\n## Best practices\n\n  * We recommend [minimap2](https://github.com/lh3/minimap2) for all long-read alignments.\n  * **Isosceles doesn't perform post-hoc splice junction correction, so it is critical to run minimap2 with the '\\-\\-junc-bed' flag.** The intron position BED file required by it can be easily created using the `gtf_to_intron_bed` function.\n  * The default settings of de novo transcript detection used by the `bam_to_tcc` function should work well for most expected read depths across eukaryotic transcriptomes, but for the analysis of spike-in data, such as SIRVs, we recommend increasing the read count threshold (the *min_read_count* argument) to a higher value (e.g. 50).\n\n## Troubleshooting\n\nYou can check if the package works correctly by running its unit tests:\n```r\ntestthat::test_package(\"Isosceles\")\n```\n\nIn case of any problems, we recommend using the Isosceles Singularity image you\ncan download from [Zenodo](https://zenodo.org/doi/10.5281/zenodo.8180648)\nor installing the package in a\n[Docker container using a Bioconductor image](https://www.bioconductor.org/help/docker).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fisosceles","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenentech%2Fisosceles","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fisosceles/lists"}