{"id":16455998,"url":"https://github.com/snikumbh/archr","last_synced_at":"2026-04-18T00:32:01.909Z","repository":{"id":69087746,"uuid":"188449833","full_name":"snikumbh/archR","owner":"snikumbh","description":"archR: Identifying promoter sequence architectures de novo using NMF","archived":false,"fork":false,"pushed_at":"2021-07-01T13:38:24.000Z","size":18596,"stargazers_count":0,"open_issues_count":2,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-10-23T08:53:09.171Z","etag":null,"topics":["archr","discovery","nmf","non-negative-matrix-factorization","promoter-sequence-architectures","r","r-package","scikit-learn","sequence-architectures","unsupervised-machine-learning"],"latest_commit_sha":null,"homepage":"https://snikumbh.github.io/archR","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/snikumbh.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","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":"2019-05-24T15:53:01.000Z","updated_at":"2021-07-01T02:07:06.000Z","dependencies_parsed_at":"2023-02-23T15:01:02.238Z","dependency_job_id":null,"html_url":"https://github.com/snikumbh/archR","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/snikumbh/archR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snikumbh%2FarchR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snikumbh%2FarchR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snikumbh%2FarchR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snikumbh%2FarchR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/snikumbh","download_url":"https://codeload.github.com/snikumbh/archR/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snikumbh%2FarchR/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31951284,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-17T17:29:20.459Z","status":"ssl_error","status_checked_at":"2026-04-17T17:28:47.801Z","response_time":62,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":["archr","discovery","nmf","non-negative-matrix-factorization","promoter-sequence-architectures","r","r-package","scikit-learn","sequence-architectures","unsupervised-machine-learning"],"created_at":"2024-10-11T10:24:23.086Z","updated_at":"2026-04-18T00:32:01.864Z","avatar_url":"https://github.com/snikumbh.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n\n# archR\n\u003c!-- badges: start --\u003e\n[![Lifecycle:\nexperimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)\n[![DOI](https://zenodo.org/badge/188449833.svg)](https://zenodo.org/badge/latestdoi/188449833)\n[![Build status](https://travis-ci.org/snikumbh/archR.svg?branch=master)](https://travis-ci.org/snikumbh/archR)\n[![Codecov test coverage](https://codecov.io/gh/snikumbh/archR/branch/master/graph/badge.svg)](https://codecov.io/gh/snikumbh/archR?branch=master)\n[![R build status](https://github.com/snikumbh/archR/workflows/R-CMD-check/badge.svg)](https://github.com/snikumbh/archR/actions)\n\u003c!-- badges: end --\u003e\n\nNote: _This package is currently under development. So, please bear with me while I put the final blocks together. Thanks for your understanding!_ \n\n\narchR is an unsupervised, non-negative matrix factorization (NMF)-based algorithm for discovery of sequence architectures de novo.\nBelow is a schematic of archR's algorithm.\n\n\u003cimg src=\"https://github.com/snikumbh/archR/blob/master/vignettes/archR_algorithm_1080p_cropped.gif\" width=\"550\" align=\"center\"\u003e\n\n\n## Installation\n\n### Python scikit-learn dependency\nThis package requires the Python module scikit-learn. Please see installation instructions [here](https://scikit-learn.org/stable/install.html).\n\n\n### To install this package, use \n\n```r\nif (!requireNamespace(\"remotes\", quietly = TRUE)) {\n    install.packages(\"remotes\")   \n}\n\nremotes::install_github(\"snikumbh/archR\", build_vignettes = FALSE)\n``` \n\n\n\n### Usage\n```r\n# load package\nlibrary(archR)\nlibrary(Biostrings)\n\n\n# Creation of one-hot encoded data matrix from FASTA file\n# You can use your own FASTA file instead\ninputFastaFilename \u003c- system.file(\"extdata\", \"example_data.fa\", \n                                  package = \"archR\", \n                                  mustWork = TRUE)\n\n# Specifying dinuc generates dinucleotide features\ninputSeqsMat \u003c- archR::prepare_data_from_FASTA(inputFastaFilename,\n                                                  sinuc_or_dinuc = \"dinuc\")\n\ninputSeqsRaw \u003c- archR::prepare_data_from_FASTA(inputFastaFilename, \n                                               raw_seq = TRUE)\n\nnSeqs \u003c- length(inputSeqsRaw)\npositions \u003c- seq(1, Biostrings::width(inputSeqsRaw[1]))\n\n# Set archR configuration\n# Most arguments have default values\narchRconfig \u003c- archR::archR_set_config(\n        parallelize = TRUE,\n        n_cores = 2,\n        n_runs = 100,\n        k_min = 1,\n        k_max = 20,\n        mod_sel_type = \"stability\",\n        bound = 10^-6,\n        chunk_size = 100,\n\tresult_aggl = \"ward.D\",\n\tresult_dist = \"euclid\",\n        flags = list(debug = FALSE, time = TRUE, verbose = TRUE,\n                     plot = FALSE)\n        )\n\n#\n### Call/Run archR\narchRresult \u003c- archR::archR(config = archRconfig,\n                               seqs_ohe_mat = inputSeqsMat,\n                               seqs_raw = inputSeqsRaw,\n                               seqs_pos = positions,\n                               total_itr = 2,\n\t\t\t       set_ocollation = c(TRUE, FALSE))\n\n```\n\n\n# Contact\nComments, suggestions, enquiries/requests are welcome! Feel free to email sarvesh.nikumbh@gmail.com or [create an new issue](https://github.com/snikumbh/archR/issues/new)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsnikumbh%2Farchr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsnikumbh%2Farchr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsnikumbh%2Farchr/lists"}