{"id":37640905,"url":"https://github.com/jkobject/genepy","last_synced_at":"2026-01-16T11:17:26.377Z","repository":{"id":50220432,"uuid":"186676304","full_name":"jkobject/genepy","owner":"jkobject","description":"A list of awesome files for computational biologists","archived":false,"fork":false,"pushed_at":"2024-01-26T16:28:11.000Z","size":25000,"stargazers_count":1,"open_issues_count":1,"forks_count":8,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-01-13T17:25:08.227Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jkobject.png","metadata":{"files":{"readme":"README.md","changelog":"HISTORY.md","contributing":"CONTRIBUTING.md","funding":".github/FUNDING.yml","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},"funding":{"github":["rochacbruno"],"patreon":null,"open_collective":null,"ko_fi":null,"tidelift":null,"community_bridge":null,"liberapay":null,"issuehunt":null,"otechie":null,"custom":null}},"created_at":"2019-05-14T18:15:37.000Z","updated_at":"2025-06-19T03:47:10.000Z","dependencies_parsed_at":"2023-09-03T11:53:44.469Z","dependency_job_id":"f8219be8-dd65-40f6-bbab-b292132f5110","html_url":"https://github.com/jkobject/genepy","commit_stats":null,"previous_names":["jkobject/genepy","jkobject/jkbio"],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/jkobject/genepy","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jkobject%2Fgenepy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jkobject%2Fgenepy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jkobject%2Fgenepy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jkobject%2Fgenepy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jkobject","download_url":"https://codeload.github.com/jkobject/genepy/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jkobject%2Fgenepy/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478188,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T06:30:42.265Z","status":"ssl_error","status_checked_at":"2026-01-16T06:30:16.248Z","response_time":107,"last_error":"SSL_read: 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":[],"created_at":"2026-01-16T11:17:25.602Z","updated_at":"2026-01-16T11:17:26.372Z","avatar_url":"https://github.com/jkobject.png","language":"Python","funding_links":["https://github.com/sponsors/rochacbruno"],"categories":[],"sub_categories":[],"readme":"[![DOI](https://zenodo.org/badge/186676304.svg)](https://zenodo.org/doi/10.5281/zenodo.10573223)\n\n# genepy\n\n_what is [genepy](https://en.wikipedia.org/wiki/G%C3%A9n%C3%A9pi)?_\n\nA set of awesome functions \u0026 tools for Computational Geneticists\n\n![long genome](documentation/genome.jpg)\n\n## Content\n\n- **utils**: where a bunch of helper functions and usefull general scripts are stored\n  - **plots**: a set of plotting tools based on [matplotlib]() and [bokeh]() to make volcano plots / CNV maps etc..\n  - **helper**: and additional helper functions to save data, do merging of dataframes...\n- **terra**: contains a set of functions that uses [dalmatian]() to interact with the [GCP]() powered genomics HPC platform: [Terra](). \n- **sequencing**: contains a set of function to works with bed/bam/fastqs...\n- **rna**: contains function to work with RNAseq (and related) data.\n  - **pyDESeq2**: it is a python integration of [deseq2]() (the differential expression analyser) with [rpy2]()\n- **mutations**: a set of functions to work with maf files, vcf files etc..\n- **google**: functions and packages linked to google's apis\n  - **google_sheet**: function to upload a df as a google sheet\n  - **gcp**: sets of functions to interact with google storage (relies on `gsutil`)\n- **epigenetics**: where we have things related to epigenomics\n  - **chipseq**: has functions to read, merge, denoise, ChIP seq data.\n  - **plot**: has functions to plot ChIP seq data.\n\n### Helper tools\n\n_tools that you do not need to use directly as they have binding functions in genepy._ \n\n- **epigenetics/rose:**: where an updated version of the rose algorithm is stored (as a git submodule) \n- **cell_line_mapping-master/python/cell_line_mapper**: a set of functions to map cell line ids to other cell line ids based on an up to date google spreadsheet. \n\n\n## Install\n\n### with conda\n\n```bash\nconda create -n genepy python=3.9\nconda activate genepy\nconda install -c bioconda bioconductor-gsva \nconda install -c bioconda bioconductor-deseq2\nconda install -c bioconda bioconductor-gseabase\nconda install -c bioconda bioconductor-erccdashboard\nconda install -c bioconda samtools\nconda install -c bioconda bwa\nconda install -c bioconda bowtie2\nconda install -c bioconda htslib\nconda install -c bioconda bedtools\n\ngit clone git://github.com/BroadInstitute/genepy.git\ncd genepy\npip install -e .\n```\n\nthen you can import files in python with e.g:\n\n```python\nfrom genepy import terra\nfrom genepy.utils import helper as h\nfrom genepy.google import gcp\nfrom genepy.utils import plot\nfrom genepy.epigenetics import chipseq\n\n```\nSome of the packages like gsheets, gcloud, firecloud-dalmatian will require you to create google accounts, login on your machine or download oauth files.\n- [gcloud](https://cloud.google.com/sdk/docs/install-sdk)\n- [firecloud-dalmatian](https://github.com/getzlab/dalmatian) \n- [gsheets](https://github.com/xflr6/gsheets)\n\n\n## data:\n\nhg38 genome sizes: from https://github.com/igvteam/igv/blob/master/genomes/sizes/hg38.chrom.sizes\n\n## About\n\nplease do contribute, we do not have time to fix all issues or work on feature requests\n\nJeremie Kalfon jkalfon@broadinstitute.org jkobject@gmail.com https://jkobject.com\n\nApache license 2.0.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjkobject%2Fgenepy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjkobject%2Fgenepy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjkobject%2Fgenepy/lists"}