{"id":29625201,"url":"https://github.com/novartis/pisces","last_synced_at":"2025-07-21T06:07:37.872Z","repository":{"id":39745077,"uuid":"317351444","full_name":"Novartis/pisces","owner":"Novartis","description":"PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.","archived":false,"fork":false,"pushed_at":"2025-06-17T17:07:41.000Z","size":18467,"stargazers_count":30,"open_issues_count":12,"forks_count":3,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-07-20T17:55:27.504Z","etag":null,"topics":["bioinformatics","bioinformatics-pipeline","rnaseq","rnaseq-pipeline","salmon","transcriptomics"],"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/Novartis.png","metadata":{"files":{"readme":"README.md","changelog":null,"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":"2020-11-30T21:33:50.000Z","updated_at":"2025-06-27T10:58:32.000Z","dependencies_parsed_at":"2024-05-28T16:14:11.832Z","dependency_job_id":null,"html_url":"https://github.com/Novartis/pisces","commit_stats":{"total_commits":119,"total_committers":6,"mean_commits":"19.833333333333332","dds":"0.10084033613445376","last_synced_commit":"9936079ac75d4b75be95bad5bc962465e8c5f458"},"previous_names":[],"tags_count":13,"template":false,"template_full_name":null,"purl":"pkg:github/Novartis/pisces","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Novartis%2Fpisces","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Novartis%2Fpisces/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Novartis%2Fpisces/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Novartis%2Fpisces/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Novartis","download_url":"https://codeload.github.com/Novartis/pisces/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Novartis%2Fpisces/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266248501,"owners_count":23899056,"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":["bioinformatics","bioinformatics-pipeline","rnaseq","rnaseq-pipeline","salmon","transcriptomics"],"created_at":"2025-07-21T06:07:37.068Z","updated_at":"2025-07-21T06:07:37.856Z","avatar_url":"https://github.com/Novartis.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![CI](https://github.com/Novartis/pisces/workflows/CI/badge.svg)](https://github.com/Novartis/pisces/actions?query=workflow%3ACI)\n[![Sphinx Docs](https://github.com/Novartis/pisces/workflows/Sphinx%20Docs/badge.svg)](https://opensource.nibr.com/pisces/)\n[![Package Builds](https://github.com/Novartis/pisces/workflows/Package%20Builds/badge.svg)](https://github.com/Novartis/pisces/actions?query=workflow%3A%22Package+Builds%22)\n[![PyPI](https://badge.fury.io/py/novartis-pisces.svg)](https://pypi.python.org/pypi/novartis-pisces)\n\n# PISCES: a package for quantitation and QC of large scale mRNA-seq datasets\n\nPISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.\n\nSee the current documentation at https://opensource.nibr.com/pisces/. Read the manuscript at https://www.biorxiv.org/content/10.1101/2020.12.01.390575v1.\n\nMatthew D Shirley, Viveksagar K Radhakrishna, Javad Golji, Joshua M Korn. (Preprint) PISCES: a package for rapid quantitation and quality control of large scale mRNA-seq datasets. bioRxiv. 2020.\n\n## Quickstart\n\nInstallation:\n```\n$ pip install --user novartis-pisces\n$ pisces_dependencies\n```\n\nSubmitting jobs to an HPC cluster:\n```\n$ pisces submit -m metadata.csv\n```\n\nSummarizing QC metrics and gene expression:\n```\n$ pisces summarize-qc -m metadata.csv -f fingerprint.txt\n$ pisces summarize-expression -m metadata.csv\n# optionally specify contrasts and formula for DESeq2 differential gene expression\n$ pisces summarize-expression -m metadata.csv -f contrasts.csv -d \"~covariate1 + covartiate2\"\n```\n\nPlease submit bugs or questions to our issue tracker.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnovartis%2Fpisces","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnovartis%2Fpisces","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnovartis%2Fpisces/lists"}