{"id":18598217,"url":"https://github.com/cmdoret/dagws_seq_algo_materials","last_synced_at":"2025-05-16T14:11:11.641Z","repository":{"id":100714874,"uuid":"317887194","full_name":"cmdoret/dagws_seq_algo_materials","owner":"cmdoret","description":"Slides and exercises from the \"Sequence Algorithms\" lectures I gave for the data analysis in genomics (DAG) workshop.","archived":false,"fork":false,"pushed_at":"2020-12-02T15:04:13.000Z","size":17851,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-02-17T23:47:35.957Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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/cmdoret.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-12-02T14:26:34.000Z","updated_at":"2020-12-30T09:41:15.000Z","dependencies_parsed_at":null,"dependency_job_id":"5a7027fa-fb72-4deb-8f34-6e10ca90856a","html_url":"https://github.com/cmdoret/dagws_seq_algo_materials","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fdagws_seq_algo_materials","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fdagws_seq_algo_materials/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fdagws_seq_algo_materials/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fdagws_seq_algo_materials/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmdoret","download_url":"https://codeload.github.com/cmdoret/dagws_seq_algo_materials/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254544159,"owners_count":22088808,"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","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":"2024-11-07T01:31:41.149Z","updated_at":"2025-05-16T14:11:11.616Z","avatar_url":"https://github.com/cmdoret.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DAGWS: Sequence algorithms lectures\n\nSlides and exercises from sequence algorithms lectures I gave for the data analysis in genomics (DAG) workshop.\n\nParts of these lectures were inspired by Ben Langmead's computational genomics classes: https://github.com/BenLangmead/comp-genomics-class\n\nAll materials in this repository is distributed under Creative Commons Attribution 4.0: You may redistribute and modify  this material however you like, just give credits :)\n\n## Structure \n\nThe course is split into 4 thematic lectures. Each lecture has an associated jupyter notebook containing exercises in python. The anwers are missing from the notebooks, but each exercise session has a separate notebook in the same folder with answers added.\n\nI: Introduction to sequence algorithms \\[[slides](slides/seq_algos_1_intro.pdf) | [exercises](exercises/notebook_session1.ipynb)\\]\n\n  * Algorithms basics\n  * Time complexity\n  * Data structures\n  * Hashing\n\nII: Sequence alignments \\[[slides](slides/seq_algos_2_seq_align.pdf) | [exercises](exercises/notebook_session2.ipynb)\\]\n\n  * Exact matching\n    - naive\n    - suffix arrays and trees\n    \n  * Inexact matching\n    - Dynamic programming\n \nIII: Computational models in genomics \\[[slides](slides/seq_algos_3_ml.pdf) | [exercises](exercises/notebook_session3.ipynb)\\]\n\n  * Markov models and HMM\n  * Classification problem\n    - Tree-based models\n    - Intro to machine learning\n \nIV: Network analysis \\[[slides](slides/seq_algos_4_markov_graphs.pdf) | [exercises](exercises/notebook_session4.ipynb)\\]\n\n  * Graph representations\n  * Graph traversal\n  * Network clustering\n\n## Contributions\nAny correction of improvement is welcome, just open an issue or PR\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdoret%2Fdagws_seq_algo_materials","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdoret%2Fdagws_seq_algo_materials","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdoret%2Fdagws_seq_algo_materials/lists"}