reademption
A pipeline for the computational evaluation of RNA-Seq data
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.7%) to scientific vocabulary
Keywords
Repository
A pipeline for the computational evaluation of RNA-Seq data
Basic Info
- Host: GitHub
- Owner: foerstner-lab
- License: other
- Language: Python
- Default Branch: main
- Homepage: https://reademption.readthedocs.io
- Size: 295 MB
Statistics
- Stars: 37
- Watchers: 8
- Forks: 19
- Open Issues: 24
- Releases: 38
Topics
Metadata Files
README.md
About
READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed to process dRNA-Seq reads (as introduced by Sharma et al., Nature, 2010) originating from bacterial samples. Meanwhile is has been extended to process data generated in different experimental setups and from all domains of life. The functions which are accessible via a command-line interface cover read processing and aligning, coverage calculation, gene expression quantification, differential gene expression analysis as well as visualization. In order to set up and perform analyses quickly READemption follows the principal of "convention over configuration": Once the input files are copied/linked into defined folders no further parameters have to be given. Still, READemption's behavior can be adapted to specific needs of the user by parameters.
Documentation
Documentation can be found on here.
Installation
Short version (if you have all the requirements installed):
$ pip install READemption
Long version including a description of the requirements and how do you get them.
License
MIT (MIT License) - see LICENSE.txt
Development
If possible follow the principal of "convention over configuration". This means input file are copied/linked into a fixed location and the resulting files are placed in fixed locations.
The classes should be path agnostic as far a possible. The controller is taking care of that and calls them adequately.
The git braching model is very close to the one proposed here. There two main branches:
- master
- dev(elopment)
And there are further supporting branches: * feature branches - branched off and back to the dev branch * release branches - branched off from dev and merged back into dev and master * hotfix branches - branched off from master and merged back into dev and master
Owner
- Name: Förstner Lab
- Login: foerstner-lab
- Kind: organization
- Location: Cologne, Germany
- Repositories: 22
- Profile: https://github.com/foerstner-lab
Research Lab of Prof. Konrad Förstner at ZB MED - Information Center for Life Sciences
GitHub Events
Total
- Issues event: 1
- Watch event: 2
Last Year
- Issues event: 1
- Watch event: 2
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 1
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- termithorbor (4)
- elhossary (3)
- gprezza (1)
- Tillsa (1)
Pull Request Authors
- konrad (1)
- elhossary (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- conda-incubator/setup-miniconda v2 composite
- ubuntu 22.04 build
- biopython >=1.79
- matplotlib >=3.5.2
- pandas >=1.4.3
- pysam >=0.19.1
- seaborn >=0.11.2
- sphinx-argparse >=0.2.5
- biopython *
- matplotlib *
- pandas *
- pysam *
- seaborn *
- sphinx-argparse *