pita
Pipeline to improve transcript annotation based on RNA-seq and ChIP-seq data.
Science Score: 23.0%
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
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○.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.0%) to scientific vocabulary
Repository
Pipeline to improve transcript annotation based on RNA-seq and ChIP-seq data.
Basic Info
Statistics
- Stars: 7
- Watchers: 2
- Forks: 1
- Open Issues: 3
- Releases: 0
Metadata Files
README.md
pita improves transcript annotation
Pipeline to improve transcript annotation based on RNA-seq and ChIP-seq data.
It has been used to annotate the Xenopus laevis genome based on experimental data.
Session et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 2016 Oct 20;538(7625):336-343. doi: 10.1038/nature19840.
However, it is not yet easy to use as the documentation is incomplete.
Overview
Pita can combine imprecise and/or incomplete gene models with experimental data such as RNA-seq and H3K4me3 ChIP-seq to create improved gene annotation. Features:
- Graph-based annotation capable of incorporating diverse types of data
- Improved annotation of 5' end of genes by prioritizing promoters with H3K4me3
- UTR annotation based on RNA-seq data in combination with change-point detection
Installation
Clone this repository:
$ git clone git@github.com/simonvh/pita.git
$ cd pita
Install dependencies via conda:
$ conda env create -f environment.yml
Activate the environment:
$ source activate pita
Test & install:
$ python setup.py test
$ python setup.py install
Owner
- Name: Simon van Heeringen
- Login: simonvh
- Kind: user
- Location: the Netherlands
- Company: @ScenicBiotech
- Repositories: 9
- Profile: https://github.com/simonvh
Principal Bioinformatician @ ScenicBiotech
GitHub Events
Total
Last Year
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Simon van Heeringen | s****n@g****m | 166 |
| Joris | j****e@s****l | 29 |
| jsteenbrugge | y****u@e****m | 26 |
| jsteenbrugge | j****e@m****l | 19 |
| Simon van Heeringen | s****n@n****l | 16 |
| Joris van Steenbrugge | j****e@h****m | 11 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 6
- Total pull requests: 8
- Average time to close issues: 23 days
- Average time to close pull requests: about 5 hours
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 0.83
- Average comments per pull request: 0.25
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Jorisvansteenbrugge (4)
- simonvh (2)
Pull Request Authors
- Jorisvansteenbrugge (7)
- simonvh (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 46 last-month
- Total dependent packages: 0
- Total dependent repositories: 2
- Total versions: 4
- Total maintainers: 2
pypi.org: pita
pita - pita improves transcript annotation
- Homepage: https://github.com/simonvh/pita
- Documentation: https://pita.readthedocs.io/
- License: MIT
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Latest release: 1.73.3
published over 10 years ago
Rankings
Dependencies
- bcbiogff
- biofluff
- biopython
- gimmemotifs 0.10.0
- htseq
- maxentscan
- networkx
- pysam
- pytest
- pyyaml
- r-changepoint
- rpy2
- sqlalchemy
- HTSeq *
- SQLAlchemy *
- bcbio-gff *
- biopython *
- gimmemotifs *
- networkx *
- numpy *
- pysam *
- pyyaml *