Portable Encapsulated Projects

All

43 repositories

pephub
Public
A web API and database for biological sample metadata
bioinformatics data-sharing metadata-management sample-metadata
TypeScript
•
BSD 2-Clause "Simplified" License
•2•16•53•0•Updated Mar 6, 2025Mar 6, 2025
pepdbagent
Public
Database for storing sample metadata
Python
•
BSD 2-Clause "Simplified" License
•1•2•8•0•Updated Mar 6, 2025Mar 6, 2025
pepspec
Public
Documentation for PEP specification and all PEPkit software
HTML
•4•9•5•0•Updated Mar 5, 2025Mar 5, 2025
looper
Public
A job submitter for Portable Encapsulated Projects
bioinformatics ngs bioinformatics-pipeline pipeline-submission-engine
Python
•
BSD 2-Clause "Simplified" License
•7•21•11•1•Updated Mar 5, 2025Mar 5, 2025
ubiquerg
Public
Tools for work (erg) everywhere (ubique)
utility-library
Python
•
BSD 2-Clause "Simplified" License
•3•0•1•0•Updated Mar 5, 2025Mar 5, 2025
geopephub
Public
Automatic uploader of GEO metadata to PEPhub.
Python
•
BSD 2-Clause "Simplified" License
•0•0•4•0•Updated Mar 3, 2025Mar 3, 2025
pipestat
Public
Pipeline results reporting package
python interface reporting postgresql pipelines results reproducibility
Python
•
BSD 2-Clause "Simplified" License
•2•4•12•0•Updated Feb 13, 2025Feb 13, 2025
pephubclient
Public
A tool to provide Python and CLI interface and Python API for PEPhub.
python bioinformatics project command-line-tool
Python
•
BSD 2-Clause "Simplified" License
•0•3•7•0•Updated Nov 26, 2024Nov 26, 2024
hello_looper
Public
A Hello World! example repository for looper
Python
•5•0•0•0•Updated Oct 2, 2024Oct 2, 2024
eido
Public
Validator for PEP objects
metadata validation conversion jsonschema pep
Python
•
BSD 2-Clause "Simplified" License
•5•5•4•0•Updated Sep 30, 2024Sep 30, 2024
peppy
Public
Project metadata manager for PEPs in Python
metadata bioinformatics ngs pipeline-submission-engine metadata-management
Python
•
BSD 2-Clause "Simplified" License
•12•37•30•1•Updated Sep 30, 2024Sep 30, 2024
geofetch
Public
Builds a PEP from SRA or GEO accessions
metadata geo download-manager sra sra-data
Python
•
BSD 2-Clause "Simplified" License
•5•46•11•0•Updated Sep 11, 2024Sep 11, 2024
pepr
Public
Project metadata manager for PEPs in R
bioinformatics metadata
R
•
Other
•1•3•2•1•Updated Aug 5, 2024Aug 5, 2024
attmap
Public
Key-value mapping that supports nested attribute-style access
Python
•
BSD 2-Clause "Simplified" License
•1•4•10•1•Updated May 10, 2024May 10, 2024
pepembed
Public
Indexer of pephub database
Python
•0•1•1•0•Updated Feb 6, 2024Feb 6, 2024
pep-pipelines
Public
Examples of how to use PEP to run pipelines with different workflow systems
Python
•0•1•1•0•Updated Dec 22, 2023Dec 22, 2023
pep-snakemake
Public archive
Example simple and bioinformatic pipelines using PEPs and snakemake.
snakemake pipeline pep
Python
•
BSD 2-Clause "Simplified" License
•1•0•0•0•Updated Dec 1, 2023Dec 1, 2023
pep-cwl
Public archive
Common Workflow Language
•0•1•0•1•Updated Dec 1, 2023Dec 1, 2023
pep-nextflow
Public archive
0•0•0•1•Updated Dec 1, 2023Dec 1, 2023
example_peps
Public
Some simple examples of PEP-compatible projects
Jupyter Notebook
•2•0•2•0•Updated Nov 16, 2023Nov 16, 2023
BiocProject
Public
BiocProject provides a PEP-compatible R package for autoloading biological data
R
•
Other
•1•3•3•1•Updated Jul 18, 2023Jul 18, 2023
pephub.databio.org
Public archive
Data stores for pephub PEPs
Shell
•0•0•2•0•Updated Jun 8, 2023Jun 8, 2023
divvy
Public
Standardized computing resource configuration
configuration-management high-performance-computing
Python
•
BSD 2-Clause "Simplified" License
•2•4•7•0•Updated Apr 24, 2023Apr 24, 2023
example-pephub-spa
Public
TypeScript
•0•0•0•0•Updated Mar 8, 2023Mar 8, 2023
example-pephub-cli
Public
Python
•0•0•0•0•Updated Mar 7, 2023Mar 7, 2023
pephub-ui
Public
TypeScript
•0•0•0•0•Updated Feb 22, 2023Feb 22, 2023
pepingester
Public
Python
•0•0•1•0•Updated Sep 3, 2022Sep 3, 2022
divcfg
Public
DIvvy computing configuration files.
Shell
•
BSD 2-Clause "Simplified" License
•3•4•2•0•Updated Aug 29, 2022Aug 29, 2022
pipestat_reader
Public
web API generator for pipeline results
graphql database api-documentation pipeline-framework results-viewer
Python
•0•0•0•0•Updated Aug 18, 2022Aug 18, 2022
pifaces
Public
A collection of looper pipeline interfaces for common tasks
BSD 2-Clause "Simplified" License
•0•0•0•0•Updated Jul 10, 2022Jul 10, 2022