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Username    nsheff
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33 projects

pepdbagent

Last released

A python-based database manager for portable encapsulated projects

refget

Last released

Python client for refget

pipestat

Last released

A pipeline results reporter

henge

Last released

Storage and retrieval of object-derived, decomposable recursive unique identifiers.

pephubclient

Last released

PEPhub command line interface.

geofetch

Last released

Downloads data and metadata from GEO and SRA and creates standard PEPs.

yacman

Last released

A standardized configuration object for reference genome assemblies

ubiquerg

Last released

Various utility functions

looper

Last released

A pipeline submission engine that parses sample inputs and submits pipelines for each sample.

genimtools

Last released

None

peppy

Last released

A python-based project metadata manager for portable encapsulated projects

piper

Last released

A lightweight python toolkit for gluing together restartable, robust command line pipelines

bedhost

Last released

A database server application that provides both a RESTful API and GUI for access to BED files and related basic statistics

bbconf

Last released

Configuration package for bedbase project

geniml

Last released

Genomic interval toolkit

eido

Last released

A project metadata validator

markmeld

Last released

Markmeld is a markup melder that combines structured yaml or markdown data into templated markdown output using jinja2.

bedboss

Last released

Pipelines for genomic region file to produce bed files, and it's statistics

lucidoc

Last released

API documentation in Markdown

pipestat-reader

Last released

A generator of pipestat-based APIs

veracitools

Last released

Testing utilities

bulker

Last released

Manager of portable multi-container computing environments

attmap

Last released

Multiple access patterns for key-value reference

refgenie

Last released

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

Last released

A standardized configuration object for reference genome assemblies

divvy

Last released

A python-based configuration manager for portable environment configurations

logmuse

Last released

Logging setup

refgenieserver

Last released

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

Last released

BED file perturbations

loopercli

Last released

A pipeline submission engine that parses sample inputs and submits pipelines for each sample.

caravel

Last released

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.

pararead

Last released

Parallel processing of sequencing reads

ngstk

Last released

Next-generation sequencing utility functions

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