{"id":21168494,"url":"https://github.com/jetbrains-research/bioinf-commons","last_synced_at":"2025-10-19T14:22:28.163Z","repository":{"id":91051065,"uuid":"173494429","full_name":"JetBrains-Research/bioinf-commons","owner":"JetBrains-Research","description":"Bioinformatics library in Kotlin","archived":false,"fork":false,"pushed_at":"2024-09-12T17:10:21.000Z","size":2549,"stargazers_count":31,"open_issues_count":1,"forks_count":3,"subscribers_count":14,"default_branch":"master","last_synced_at":"2024-09-13T19:59:41.606Z","etag":null,"topics":["2bit","bam","bed","bioinformatics","cancellable","chip-seq","dataframe","dataset","dna-sequence","fasta","fastq","hmm","hypothesis-testing","kotlin","methylation","mixture","progress","sampling"],"latest_commit_sha":null,"homepage":"","language":"Kotlin","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/JetBrains-Research.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES.txt","contributing":null,"funding":null,"license":"LICENSE.txt","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":"2019-03-02T20:15:30.000Z","updated_at":"2024-09-12T17:10:25.000Z","dependencies_parsed_at":"2023-03-01T17:00:14.503Z","dependency_job_id":"3fb61389-8e0a-4e58-b08d-0f4b306e4246","html_url":"https://github.com/JetBrains-Research/bioinf-commons","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/JetBrains-Research%2Fbioinf-commons","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JetBrains-Research%2Fbioinf-commons/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JetBrains-Research%2Fbioinf-commons/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JetBrains-Research%2Fbioinf-commons/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JetBrains-Research","download_url":"https://codeload.github.com/JetBrains-Research/bioinf-commons/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225578917,"owners_count":17491283,"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":["2bit","bam","bed","bioinformatics","cancellable","chip-seq","dataframe","dataset","dna-sequence","fasta","fastq","hmm","hypothesis-testing","kotlin","methylation","mixture","progress","sampling"],"created_at":"2024-11-20T15:14:35.473Z","updated_at":"2025-10-19T14:22:28.141Z","avatar_url":"https://github.com/JetBrains-Research.png","language":"Kotlin","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![JetBrains Research](https://jb.gg/badges/research.svg)](https://confluence.jetbrains.com/display/ALL/JetBrains+on+GitHub)\n[![license](https://img.shields.io/github/license/mashape/apistatus.svg)](https://opensource.org/licenses/MIT)\n[![tests](http://teamcity.jetbrains.com/app/rest/builds/buildType:(id:Biolabs_BioinfCommons)/statusIcon.svg)](http://teamcity.jetbrains.com/viewType.html?buildTypeId=Biolabs_BioinfCommons\u0026guest=1)\n\nBioinf-commons\n==============\nBioinformatics library in [Kotlin](https://kotlinlang.org).\n\nContents\n--------\n\n* `org.jetbrains.bio.dataframe` - Pandas like dataframe\n* `org.jetbrains.bio.experiment` - Named computation - experiment and resources configuration\n* `org.jetbrains.bio.genome` - APIs for working with Genome, Sequence, Genes, Ontologies etc.\n    * `containers` - Genome location sets API\n    * `coverage` - Genome coverage API, paired/single end, fragment size estimation\n    * `data` - Describe any kind of dataset resources including replicates\n    * `format` - Bam (including Bisulfite sequencing), Bed, Fasta, Fastq, 2bit formats support\n    * `methylome` - API to work with methylomes - filtration, statistics, aggregations etc.\n    * `query` - Named functions - queries with caching capabilities\n    * `sampling` - API for genomic sampling - sequencies, locations, etc.\n    * `sequence` - Genome sequence API\u003cbr/\u003e\n      Also: Biomart, Ensembl, UCSC support, Genomes and Genes annotations\n* `org.jetbrains.bio.statistics` - Statistics utilities including distributions mixtures, hmms and hypothesis testing\n* `org.jetbrains.bio.util` - Cancellable computations, progress reporters, logging utilities, and other utils\n\nTests\n-----\n\n   ```bash\n   $ ./gradlew clean test --no-daemon --max-workers 1\n   ```\n\nUsages\n------\nUsed in the following projects:\n\n* [Omnipeak](https://github.com/JetBrains-Research/omnipeak) Universal chromatin peak caller\n* [JBR](https://github.com/JetBrains-Research/jbr) JBR Genome Browser\n* [FARM](https://github.com/JetBrains-Research/fishbone) hierarchical association rule mining and visualization method\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjetbrains-research%2Fbioinf-commons","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjetbrains-research%2Fbioinf-commons","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjetbrains-research%2Fbioinf-commons/lists"}