32 projects
bedboss
Pipelines for genomic region file to produce bed files, and it's statistics
bbconf
Configuration package for bedbase project
eido
A project metadata validator
henge
Storage and retrieval of object-derived, decomposable recursive unique identifiers.
pararead
Parallel processing of sequencing reads
pepdbagent
A python-based database manager for portable encapsulated projects
refget
Python client for refget
pephubclient
PEPhub command line interface.
geofetch
Downloads data and metadata from GEO and SRA and creates standard PEPs.
geniml
Genomic interval toolkit
peppy
A python-based project metadata manager for portable encapsulated projects
ubiquerg
Various utility functions
yacman
A standardized configuration object for reference genome assemblies
pipestat
A pipeline results reporter
looper
A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
piper
A lightweight python toolkit for gluing together restartable, robust command line pipelines
bedms
BEDMess attribute standardizer for metadata attribute standardization
logmuse
Logging setup
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
attmap
Multiple access patterns for key-value reference
refgenie
Refgenie creates a standardized folder structure for reference genome files and indexes. You can download pre-built genomes or build your own for any fasta file
refgenconf
A standardized configuration object for reference genome assemblies
refgenieserver
This server provides both a web interface and a RESTful API. Users may explore and download archived indexes from the web interface or develop tools that programmatically query the API.
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.
