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https://github.com/clinical-genomics/fusion-report

Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/

https://github.com/clinical-genomics/fusion-report

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.9%) to scientific vocabulary

Keywords

fusion-genes report visualization
Last synced: 5 months ago · JSON representation

Repository

Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/

Basic Info
  • Host: GitHub
  • Owner: Clinical-Genomics
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 23.4 MB
Statistics
  • Stars: 26
  • Watchers: 4
  • Forks: 12
  • Open Issues: 4
  • Releases: 24
Topics
fusion-genes report visualization
Created almost 7 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog License

README.md

fusion-report

install with bioconda build Codacy Badge DOI Slack Status

This python script generates an interactive summary report from fusion detection tools. Fusion-report is part of a bigger project nf-core/rnafusion which is designed to detect and report fusion genes from RNA-seq data.

TL;DR: Live demo here.

Supported tools

Installation

Using Conda

bash conda install -c bioconda fusion-report

From source

```bash

sqlite3 can be installed via conda/mamba as well

sudo apt-get install sqlite3 pip3 install -r requirements.txt && python3 setup.py install ```

Usage

```bash

Download required databases

Currently supported databases: FusionGDB2, Mitelman and COSMIC

COSMIC requires login credentials to download Fusion gene Database

fusionreport download --cosmicusr '' --cosmic_passwd '' /path/to/db/

Run the fusion-report

fusionreport run "" /path/to/output /path/to/db/ \ --arriba tests/testdata/arriba.tsv \ --dragen tests/testdata/dragen.tsv \ --ericscript tests/testdata/ericscript.tsv \ --fusioncatcher tests/testdata/fusioncatcher.txt \ --pizzly tests/testdata/pizzly.tsv \ --squid tests/testdata/squid.txt \ --starfusion tests/testdata/starfusion.tsv \ --jaffa tests/test_data/jaffa.csv \ --allow-multiple-gene-symbols # in case gene symbol in fusion can't be determined, treat each provided fusion as a separate one. ```

Or get help and list all possible parameters.

bash fusion_report --help fusion_report run --help fusion_report download --help fusion_report sync --help

For more info on how to run the script, please see the documentation.

Credits

Owner

  • Name: Clinical Genomics
  • Login: Clinical-Genomics
  • Kind: organization
  • Location: Stockholm, Sweden

GitHub Events

Total
  • Create event: 8
  • Issues event: 2
  • Release event: 4
  • Watch event: 4
  • Issue comment event: 1
  • Push event: 20
  • Pull request review comment event: 11
  • Pull request review event: 11
  • Pull request event: 8
  • Fork event: 2
Last Year
  • Create event: 8
  • Issues event: 2
  • Release event: 4
  • Watch event: 4
  • Issue comment event: 1
  • Push event: 20
  • Pull request review comment event: 11
  • Pull request review event: 11
  • Pull request event: 8
  • Fork event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 44
  • Total pull requests: 38
  • Average time to close issues: 5 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 24
  • Total pull request authors: 12
  • Average comments per issue: 1.41
  • Average comments per pull request: 0.37
  • Merged pull requests: 22
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 1
  • Pull requests: 8
  • Average time to close issues: 1 day
  • Average time to close pull requests: 8 days
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.25
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • matq007 (15)
  • valleema (3)
  • ewels (2)
  • rannick (2)
  • marchoeppner (2)
  • anoronh4 (2)
  • suhrig (1)
  • widfa11 (1)
  • jingwangiub (1)
  • shwcha9 (1)
  • chaoyanggu (1)
  • ChiBia (1)
  • gybeata (1)
  • Rmulet (1)
  • yuifu (1)
Pull Request Authors
  • rannick (17)
  • matq007 (7)
  • seallard (6)
  • pintoa1-mskcc (3)
  • codacy-badger (2)
  • gatoravi (2)
  • MikeWLloyd (2)
  • apeltzer (2)
  • tijeco (1)
  • dependabot[bot] (1)
  • HaidYi (1)
  • chadisaad (1)
Top Labels
Issue Labels
bug (7) enhancement (6) Waiting For Review (3) documentation (3) good first issue (2) question (2) help wanted (1) feature-request (1) invalid (1)
Pull Request Labels
Waiting For Review (1) dependencies (1) python (1)

Dependencies

requirements-dev.txt pypi
  • flake8 * development
  • isort * development
  • mypy ==0.701 development
  • setuptools * development
requirements.txt pypi
  • Jinja2 >=2.10
  • MarkupSafe *
  • colorlog *
  • openpyxl *
  • pandas *
  • python-rapidjson *
  • pyyaml >=4.2b1
  • tqdm *
  • xlrd >=1.0.0
Dockerfile docker
  • python 3.9.7 build
.github/workflows/bump_version.yml actions
  • Clinical-Genomics/bump2version-ci v3 composite
.github/workflows/integration_tests.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
.github/workflows/lint.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • psf/black stable composite
.github/workflows/publish_image.yml actions
  • actions/checkout v3 composite
  • docker/build-push-action v3 composite
  • docker/login-action v2 composite
  • docker/setup-buildx-action v2 composite
setup.py pypi
pyproject.toml pypi