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GitHub / czbiohub-sf / cerebra

A tool for fast and accurate summarizing of variant calling format (VCF) files

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/czbiohub-sf%2Fcerebra

Stars: 59
Forks: 9
Open Issues: 10

License: mit
Language: Python
Repo Size: 164 MB
Dependencies: 44

Created: about 5 years ago
Updated: 3 months ago
Last pushed: over 1 year ago
Last synced: 1 day ago

Topics: genomics, mutations, scrna-seq, variant-calling

Files

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Readme

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Dependencies

requirements.txt pypi

biopython ==1.77
click *
cython ==0.29.13
hgvs *
ncls *
numpy *
pandas *
pathos *
pyfaidx *
setuptools >=38.6.0
tqdm *
vcfpy *

requirements_versioned.txt pypi

biopython ==1.77
click ==7.0
cython ==0.29.13
hgvs ==1.4.0
ncls ==0.0.51
numpy ==1.18.1
pandas ==0.25.3
pathos ==0.2.5
pyfaidx ==0.5.6
setuptools ==47.3.1
tqdm ==4.42.0
vcfpy ==0.12.1

test_requirements.txt pypi

coverage * test
flake8 * test
pytest * test

environment.yml conda

ca-certificates 2020.6.24
certifi 2020.6.20
libcxx 10.0.0
libedit 3.1.20191231
libffi 3.3
ncurses 6.2
openssl 1.1.1g
pip 20.1.1
python 3.7.7
readline 8.0
setuptools 49.2.0
sqlite 3.32.3
tk 8.6.10
wheel 0.34.2
xz 5.2.5
zlib 1.2.11

Dockerfile docker

ubuntu latest build