https://github.com/beardymcjohnface/autocircexplorer
Science Score: 26.0%
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
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○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 (4.8%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: beardymcjohnface
- Language: Perl
- Default Branch: master
- Size: 53.7 KB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
autoCircExplorer
Run CIRCexplorer2 and rmats-turbo but better.
Install
```shell
OPTIONAL: set up an env
conda create -n autoce2 python=3.12 conda activate autoce2
clone the repo
git clone https://github.com/beardymcjohnface/autocircexplorer.git
install with pip
cd autocircexplorer/ pip install -e . ```
Run
Run rmats individually
Make sure your sequencing reads are all in one directory, or pass a sample.tsv file.
shell
autoce2 run \
--input1 fastqDir/ \
--ref starRefDir/ \
--gtf refGenes.gtf \
rmats
Compare two groups
Pass separate directories or sample files for each sample group.
shell
autoce2 run \
--input1 group1Fastq/ \
--input2 group2Fastq/ \
--ref starRefDir/ \
--gtf refGenes.gtf \
rmats
Run circexplorer2 and ciri2
ciri2 needs: --fa
circexplorer2 needs: --fa, --gtf, and --ref
shell
autoce2 run \
--input1 fastq/ \
--fa genome.fasta \
--gtf genes.gtf \
--ref star_index/ \
ciri2 ce2
GitHub Events
Total
- Watch event: 1
- Public event: 1
- Push event: 3
Last Year
- Watch event: 1
- Public event: 1
- Push event: 3
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total 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
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