https://github.com/ccicb/juncseek
Science Score: 13.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: CCICB
- Language: Python
- Default Branch: main
- Size: 9.77 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
JuncSeq
JuncSeq is a bioinformatics tool designed to detect and analyse aberrant splicing events using splice junction data. It enables researchers to: 1. Identify aberrant splicing in a predefined list of genes. 2. Detect splice junction abnormalities near specific genetic variants.
Installation
You can install JuncSeek directly from GitHub:
sh
pip install git+https://github.com/CCICB/juncseek.git
Alternatively, you can clone the repository and install it in editable mode:
sh
git clone https://github.com/CCICB/juncseek.git
cd juncseek
pip install --editable .
Usage
Once installed, you can run juncseek from the command line as follows:
sh
juncseek [-h] --patient-list PATIENT_LIST --gtf GTF [--gene-list GENE_LIST] [--vcf VCF] --output OUTPUT
Arguments:
--patient-list PATIENT_LIST: Path to the patient list file (only needs paths as input).--gtf GTF: Path to the GTF annotation file.--gene-list GENE_LIST(optional) : Path to the gene list file.--vcf VCF(optional) : Path to the VCF file containing variant data.--output OUTPUT: Path to the output directory.
Owner
- Name: CCICB
- Login: CCICB
- Kind: organization
- Repositories: 4
- Profile: https://github.com/CCICB
GitHub Events
Total
- Delete event: 1
- Member event: 1
- Push event: 6
- Pull request event: 1
- Create event: 3
Last Year
- Delete event: 1
- Member event: 1
- Push event: 6
- Pull request event: 1
- Create event: 3
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 0
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- pj-sullivan (1)
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