PEPkit: the bio data management toolkit
Initializing search
PEP specification
Eido
GEOfetch
Looper
PEPhub
Peppy
Pipestat
Pypiper
How to cite
Stats
PEPkit: the bio data management toolkit
PEP specification
PEP specification
Getting started
Getting started
A simple example
PEP specification
Rationale
Detailed how-to guides
Detailed how-to guides
Specify multi-value attributes
Eliminate paths from table
Remove genome from table
Store many projects in one file
Create automatic groups
Mix & match amendments
Import plus amendments
Create a PEP from GEO/SRA
Validate a PEP
Implementations
Implementations
Python package: peppy
R package: pepr
Reference
Reference
How to cite
Changelog
PEPkit usage statistics
Support
Team and Contributing
Eido
Eido
Getting started
Getting started
Install and configure
How-to guides
How-to guides
Tutorial: eido in Python
Tutorial: eido in a shell
Using eido filters
Writing a custom filter
Writing a schema
Reference
Reference
How to cite
Example schemas
Eido Python API
Built-in filters API
Support
Contributing
Changelog
GEOfetch
GEOfetch
Getting started
Getting started
Install and configure
SRA convert
Tutorials
Tutorials
Tutorial for processed data
Tutorial for raw data
geofetch from within Python
GSE Finder
How-to guides
How-to guides
Specifying samples to download
Set SRA data download location
Run SRA convert
Reference
Reference
How to cite
API
Metadata output
CLI usage
FAQ
Support
Contributing
Changelog
Looper
Looper
Getting started
Getting started
Features at-a-glance
Hello world
How-to guides
How-to guides
Defining a project
Details of a project
Running a pipeline
Initializing a repository
Using pipestat
Parameterizing pipelines
Running on a cluster
Grouping many jobs into one
Running jobs in containers
Handling multiple input files
Running multiple pipelines
Writing a pipeline interface
Using looper config
Using geofetch
Browsable HTML Reports
Using divvy
Using divvy
Configuring divvy
Tutorial: divvy in python
Tutorial: divvy on the command line
Configuring containers
Configuring connection with client software
Default packages
DIVCFG examples
Reference
Reference
How to cite
Pipeline interface specification
Pipeline tiers
Concentric templates
Pre-submission hooks system
Looper variable namespaces
Advanced features
Usage
Configuration files
API
FAQ
Support
Contributing
Changelog
PEPhub
PEPhub
User guide
User guide
Getting started
Creating an account and logging in
Uploading your first PEP
Use a PEP in an existing pipeline
Developer guide
Developer guide
Setup
Deployment
Development
Authentication
Authentication Device
Semantic search
PEPHubClient
PEPHubClient
Changelog
Python API
CLI usage
Server settings
PEPembed
PEPembed
pepdbagent
pepdbagent
Database tutorial
Changelog
geopephub
Reference
Reference
Schema registry
How to cite
Changelog
Peppy
Peppy
Getting started
Getting started
Installing and Hello World
How-to guides
How-to guides
How to initialize a Project
How to use peppy
How to use subsample table
How to use amendments
How to use append sample modifier
How to use imply sample modifier
How to validate a PEP
Reference
Reference
Project models
How to cite
API
Support
Contributing
Changelog
Pipestat
Pipestat
How-to guides
How-to guides
Quickstart
Write a pipestat schema
Use Python API
Use command line interface
Report objects as results
Configure pipestat
Reference
Reference
How to cite
CLI usage
Configuration format
Testing configuration
Environment variables
Pipestat specification
Python API
Support
Contributing
Changelog
Pypiper
Pypiper
Getting started
Getting started
Philosophy
Features at-a-glance
Hello world
Developer guides
Developer guides
Building a basic pipeline
Using the run method
Automatic command-line arguments
Configuring pipelines
Reporting statistics
Reporting statistics with pipestat
Cleaning up intermediate files
Best practices
Toolkits
Toolkits
NGSTk: the NGS toolkit
Reference
Reference
How to cite
Catalog of pipeline outputs
Pypiper API
NGSTk API
FAQ
Support
Contributing
Changelog
How to cite
Stats
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