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

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-old-fork

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary
Last synced: 9 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: 20.3 MB
Statistics
  • Stars: 1
  • Watchers: 0
  • Forks: 1
  • Open Issues: 0
  • Releases: 6
Fork of Clinical-Genomics/fusion-report
Created over 4 years ago · Last pushed over 2 years 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=2.1.4

From source

bash sudo apt-get install sqlite3 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
  • Member event: 1
Last Year
  • Member event: 1

Dependencies

.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
.github/workflows/pr.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
.github/workflows/release.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
  • peaceiris/actions-gh-pages v3 composite
Dockerfile docker
  • python 3.9.7 build
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