{"id":21662826,"url":"https://github.com/higlass/clodius","last_synced_at":"2025-04-05T08:03:45.380Z","repository":{"id":9366307,"uuid":"56856815","full_name":"higlass/clodius","owner":"higlass","description":"Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.","archived":false,"fork":false,"pushed_at":"2025-02-22T05:33:03.000Z","size":28238,"stargazers_count":39,"open_issues_count":40,"forks_count":21,"subscribers_count":13,"default_branch":"develop","last_synced_at":"2025-03-29T07:05:29.791Z","etag":null,"topics":["gehlenborglab","hi-c","higlass"],"latest_commit_sha":null,"homepage":"","language":"Python","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/higlass.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.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":"2016-04-22T13:20:09.000Z","updated_at":"2025-02-22T05:33:07.000Z","dependencies_parsed_at":"2025-01-20T14:35:50.212Z","dependency_job_id":null,"html_url":"https://github.com/higlass/clodius","commit_stats":null,"previous_names":[],"tags_count":80,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fclodius","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fclodius/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fclodius/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fclodius/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/higlass","download_url":"https://codeload.github.com/higlass/clodius/tar.gz/refs/heads/develop","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247305930,"owners_count":20917207,"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":["gehlenborglab","hi-c","higlass"],"created_at":"2024-11-25T10:18:15.935Z","updated_at":"2025-04-05T08:03:45.349Z","avatar_url":"https://github.com/higlass.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Clodius\n\n[![Python](https://img.shields.io/pypi/v/clodius)](https://pypi.org/project/clodius)\n[![Build Status](https://travis-ci.org/higlass/clodius.svg?branch=develop)](https://travis-ci.org/higlass/clodius)\n[![Docs](https://img.shields.io/badge/docs-📖-red.svg?colorB=6680ff)](https://docs.higlass.io/data_preparation.html)\n\nDisplaying large amounts of data often requires first turning it into\nnot-so-large amounts of data. Clodius is a program and library designed\nto aggregate large datasets to make them easy to display at different\nresolutions.\n\n## Demo\n\nInstall the clodius package:\n\n```shell\npip install clodius\n```\n\nAnd use it aggregate a bigWig file:\n\n```shell\ncurl https://raw.githubusercontent.com/hms-dbmi/clodius/develop/test/sample_data/geneAnnotationsExonsUnions.short.bed \\\n  \u003e /tmp/sample.short.bed\nclodius aggregate bedfile /tmp/sample.short.bed\n```\n\nThe output files can then be displayed using [higlass-manage](https://github.com/higlass/higlass-manage). For more information about viewing these types of files take a look at the [higlass docs](https://docs.higlass.io).\n\n[More examples](COMMANDS.md) are available.\n\n## File Types\n\n- Non-genomic Rasters\n  - [TSV Files](docs/raster/tsv.rst)\n- Genomic Data\n  - [Bed Files](docs/genomic/bed.rst)\n  - [BedGraph Files](docs/genomic/bedgraph.rst)\n  - [Bedpe-like Files](docs/genomic/bedpe.rst)\n  - [BigBed Files](docs/genomic/bigbed.rst)\n  - [BigWig Files](docs/genomic/bigwig.rst)\n  - [Chromosome Sizes](docs/genomic/chromosome-sizes.rst)\n  - [Cooler Files](docs/genomic/cooler.rst)\n  - [Gene Annotation](docs/genomic/gene-annotation.rst)\n  - [HiTile Files](docs/genomic/hitile.rst)\n  - [Multivec Files](docs/genomic/multivec.rst)\n\n## Development\n\n\nThe recommended way to develop `clodius` is to use a [conda](https://conda.io/docs/intro.html) environment and\ninstall `clodius` with develop mode:\n\n```shell\npip install -e \".[dev]\"\n```\n\n## Testing\n\n\nThe unit tests for clodius can be run using [pytest](https://docs.pytest.org/en/latest/):\n\n```shell\npytest\n```\n\nIndividual unit tests can be specified by indicating the file and function\nthey are defined in:\n\n```shell\npytest test/cli_test.py:test_clodius_aggregate_bedgraph\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fclodius","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhiglass%2Fclodius","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fclodius/lists"}