https://github.com/dib-lab/dammit

just annotate it, dammit!
https://github.com/dib-lab/dammit

annotation bioinformatics transcriptomics

Last synced: 15 days ago
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just annotate it, dammit!

• Host: GitHub
• URL: https://github.com/dib-lab/dammit
• Owner: dib-lab
• License: other
• Created: 2015-09-18T09:22:12.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2023-08-22T18:53:56.000Z (over 2 years ago)
• Last Synced: 2026-01-08T00:36:56.685Z (26 days ago)
• Topics: annotation, bioinformatics, transcriptomics
• Language: Python
• Homepage: http://dib-lab.github.io/dammit/
• Size: 12.1 MB
• Stars: 93
• Watchers: 11
• Forks: 28
• Open Issues: 79
• Metadata Files:
  • Readme: README.md
  • Changelog: ChangeLog
  • License: LICENSE
  • Citation: CITATION

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README

          
[![image](https://travis-ci.org/dib-lab/dammit.svg)](https://travis-ci.org/dib-lab/dammit)

[![Documentation Status](https://readthedocs.org/projects/dammit/badge/)](http://dammit.readthedocs.io/en/latest)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3569831.svg)](https://doi.org/10.5281/zenodo.3569831)

*"I love writing BLAST parsers!" -- no one, ever*

dammit is a simple de novo transcriptome annotator. It was born out of

the observation that: annotation is mundane and annoying; all the

individual pieces of the process exist already; and, the existing

solutions are overly complicated or rely on crappy non-free software.

Science shouldn't suck for the sake of sucking, so dammit attempts to

make this sucky part of the process suck a little less.

## Basic Usage

Install dammit with bioconda.

    conda create -n dammit-env python=3 dammit

    conda activate dammit-env

Download and install a subset of the databases:

    dammit databases --install --quick

And the annotate with:

    dammit annotate 

Head over to the [docs](http://dib-lab.github.io/dammit/) for much more detailed

information!

## Acknowledgements

I've received input and advice from a many sources, including but

probably not limited to: C Titus Brown, Matt MacManes, Chris Hamm,

Michael Crusoe, Russell Neches, Luiz Irber, Lisa Cohen, Tessa Pierce,

Sherine Awad, and Tamer Mansour.

CS was funded by the National Human Genome Research Institute of the

National Institutes of Health under Award Number R01HG007513 through May

2016, and now receives support from the Gordon and Betty Moore

Foundation under Award number GBMF4551.