32 projects
bedboss
Pipelines for genomic region file to produce bed files, and its statistics
bbconf
Configuration and data management tool for BEDbase
ubiquerg
Various utility functions
peppy
A python-based project metadata manager for portable encapsulated projects
refgenconf
A standardized configuration object for reference genome assemblies
looper
A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
geofetch
Downloads data and metadata from GEO and SRA and creates standard PEPs.
attmap
Multiple access patterns for key-value reference
refget
GA4GH refget - reference sequence and sequence collection tools
pephubclient
PEPhub command line interface.
piper
A lightweight python toolkit for gluing together restartable, robust command line pipelines
pipestat
A pipeline results reporter
logmuse
Logging setup
yacman
A YAML configuration manager
refgenieserver
A web interface and RESTful API for reference genome assets
refgenie
Refgenie creates a standardized folder structure for reference genome files and indexes
henge
Storage and retrieval of object-derived, decomposable recursive unique identifiers.
eido
A project metadata validator
pararead
Parallel processing of sequencing reads
pepdbagent
A python-based database manager for portable encapsulated projects
geniml
Genomic interval toolkit
bedms
BEDMess attribute standardizer for metadata attribute standardization
bedhost
A database server application that provides both a RESTful API and GUI for access to BED files and related basic statistics
markmeld
Markmeld is a markup melder that combines structured yaml or markdown data into templated markdown output using jinja2.
lucidoc
API documentation in Markdown
bulker
Manager of portable multi-container computing environments
bedshift
BED file perturbations
ngstk
Next-generation sequencing utility functions
4 archived projects
pipestat-reader Archived
A generator of pipestat-based APIs
veracitools Archived
Testing utilities
divvy Archived
A python-based configuration manager for portable environment configurations
caravel Archived
Caravel provides aweb interface to interact with your PEP-formatted projects. Caravel lets you submit jobs to any cluster resource manager, monitor jobs, summarize results, and browse project summary web pages.
