{"id":19749535,"url":"https://github.com/mskcc/agreto","last_synced_at":"2026-05-11T21:38:04.592Z","repository":{"id":189842063,"uuid":"681357041","full_name":"mskcc/agReto","owner":"mskcc","description":"Find wild-type sequences of neoantigens and run netMHCpan","archived":false,"fork":false,"pushed_at":"2023-08-22T02:09:48.000Z","size":4117,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-06-20T21:01:59.270Z","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/mskcc.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":"2023-08-21T20:50:15.000Z","updated_at":"2023-08-22T01:06:35.000Z","dependencies_parsed_at":"2023-08-22T02:59:14.655Z","dependency_job_id":null,"html_url":"https://github.com/mskcc/agReto","commit_stats":null,"previous_names":["mskcc/agreto"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/mskcc/agReto","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FagReto","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FagReto/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FagReto/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FagReto/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/agReto/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FagReto/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":285859613,"owners_count":27243729,"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":"2025-11-22T02:00:05.934Z","response_time":64,"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":"2024-11-12T02:27:08.477Z","updated_at":"2025-11-22T21:03:31.843Z","avatar_url":"https://github.com/mskcc.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# agReto\nThis package contains utilities for finding wild-type sequences of neoantigens and running netMHCpan on them. The affinity data obtained can be used to estimate agretopicity (ratio of mutant vs. wild-type peptide binding affinities).\n\n## Regenerating wild-type sequences of neoantigens\n\nThe function [wildtype](man/wildtype.Rd) attemps to regenerate wild-type sequences of a set of neoantigens solely based on neoantigen sequences along with the gene name and identity of mutations (expressed in `HGVSp_short` notation; hg19 genome assumed). The input file is taken into the argument `neoag`, where the expected column names are `peptide`, `gene`, and `mutation`:\n\n| peptide     | gene  | mutation | hla         |\n| ----------- | ----- | -------- | ----------- |\n| DYNWLIYHL   | DHX36 | p.H882D  | HLA-A*24:02 |\n| YGLFVTRAL   | EIF3H | p.S127L  | HLA-C*12:03 |\n| ...         | ...   | ...      | ...         |\n\nAn example file can be seen in [input_data.txt](example/data/input_data.txt). The column `hla` above is not necssary for this call but will just be carried over into the output. The other argument to `wildtype` is a list of all known protein sequences with each element named by gene name (Hugo symbol). It defaults to an object shipped within the package [z.rds](inst/extdata/z.rds). Any queries for genes not in this list will return `NA`. \n\nA call like the following:\n```\nlibrary(agReto)\nx \u003c- read.table('input_data.txt', header = TRUE, sep = '\\t')\nz \u003c- wildtype(neoag = x)\nhead(z)\n```\n\nwould produce\n\n| peptide     | gene  | mutation | hla         |     wt    |     \n| ----------- | ----- | -------- | ----------- | --------- |\n| DYNWLIYHL   | DHX36 | p.H882D  | HLA-A*24:02 | HYNWLIYHL | \n| YGLFVTRAL   | EIF3H | p.S127L  | HLA-C*12:03 | YGSFVTRAL |\n| ...         | ...   | ...      | ...         | ...       |\n\nNote that any mutations that are non-SNVs would also generate `NA`s. It is best to filter them out first.\n\n## Binding affinity prediction for peptides\n\nFor convenience in estimating agretopicity (relative affinity of neoantigens with respect to their wild-type counterparts), a function [netmhc](man/netmhc.Rd) for calling [netMHCpan](https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/) on a single peptide (wild-type in this context but could be arbitrary peptides) and a wrapper [run.netmhc](man/run.netmhc.Rd) for multiple peptides are provided. \n\nThe single-peptide function can be called, e.g., by\n\n```\ndir \u003c- '/juno/work/ccs/wooh/pkgs/netMHCpan-4.1/Linux_x86_64'\nb1 \u003c- netmhc(peptide = 'HYNWLIYHL', hla = 'HLA-A*24:02', netmhc.dir = dir)\nb1\n```\nThe path `netmhc.dir` is the main directory path of the [netMHCpan](https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/). The path shown above works on `juno` (needs to be linux; NOT on remote-mounted mac).\n\nThe output `b1` is a formated data frame of the standard netMHCpan output.\n\nTo call the wrapper, put together a data frame with two columns `peptide` and `hla`:\n\n| peptide   | hla         |\n| --------- | ----------- |\n| HYNWLIYHL | HLA-A*24:02 |\n| YGSFVTRAL | HLA-C*12:03 |\n| ...       | ...         |\n\nand call it by\n\n```\ninput \u003c- data.frame(peptide = z$wt, hla = z$hla)\nb \u003c- run.netmhc(input, netmhc.dir = dir)\n```\n\nThe output `b` is a multi-row data frame version of `b1` above.\n\nSee [example](example/run.R) for further information.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fagreto","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Fagreto","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fagreto/lists"}