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docs
docs
 
 
examples
examples
 
 
genie
genie
 
 
git-hooks
git-hooks
 
 
.gitignore
.gitignore
 
 
.ruffconfig
.ruffconfig
 
 
CODEOWNERS
CODEOWNERS
 
 
CONTRIBUTING.md
CONTRIBUTING.md
 
 
LICENSE
LICENSE
 
 
README.md
README.md
 
 
consortium_13.4_config.json
consortium_13.4_config.json
 
 
create_panel_tested_positions_cache.py
create_panel_tested_positions_cache.py
 
 
create_panel_tested_positions_cache_consortium.py
create_panel_tested_positions_cache_consortium.py
 
 
create_vcf.py
create_vcf.py
 
 
create_vcf_consortium.py
create_vcf_consortium.py
 
 
extract_sequences.py
extract_sequences.py
 
 
fix_gene_panels.py
fix_gene_panels.py
 
 
fix_gene_panels_consortium.py
fix_gene_panels_consortium.py
 
 
genie_create_aux_files.ipynb
genie_create_aux_files.ipynb
 
 
genie_create_aux_files_consortium.ipynb
genie_create_aux_files_consortium.ipynb
 
 
mkdocs.yml
mkdocs.yml
 
 
normalize_vcf.sh
normalize_vcf.sh
 
 
normalize_vcf_consortium.sh
normalize_vcf_consortium.sh
 
 
run_ica.sh
run_ica.sh
 
 
run_ica_docker.sh
run_ica_docker.sh
 
 
setup.py
setup.py
 
 

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Python module genie

This Python module is for working with data from the AACR genie project. Please see the docmentation at https://Bayer-Group.github.io/genie-parser/ for details.

!!! warning

If you want to contribute to this project by pushing any commits, please copy the git hooks to .git/hooks. This is not automatically done by a git clone. See the README in the git-hooks directory.

Installation of the genie package

It is recommended to create a new virtual environment with Python >= 3.9 and to install the genie package in that environment. Activate the environment and run:

pip install "git+https://github.com/Bayer-Group/genie-parser.git"

If you want to install a particular develpment branch, use

pip install "git+https://github.com/Bayer-Group/genie-parser.git@BRANCHNAME"

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Python package for processing AACR GENIE data

bayer-group.github.io/genie-parser/

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bayer-reg-nonebeat-not-applicableopen-source

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