Sars Cov 2 Python Packages

seirsplus

Models of SEIRS epidemic dynamics with extensions, including network-structured populations, testing, contact tracing, and social distancing.

relecov-tools

set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to public databases, as well as analysis runs and database storage.

pyross

PyRoss: inference, forecasts, and optimised control of epidemiological models in Python. github.com/rajeshrinet/pyross

covid19-py

🦠See COVID-19 data from the command line

bioexplorer

The Blue Brain BioExplorer (BBBE) is a tool for data visualization experts and scientists to extract and analyze scientific data from visualization and interactive exploration

sc2ts

ARG inference and analysis utilities for pandemic-scale SARS-CoV-2 data

pyncov

Pyncov-19 is a tiny probabilistic simulator for SARS-CoV-2

python-outbreak-info

Python package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info

sars2seq

A Python library and command-line scripts for working with SARS-CoV-2 sequences

covsonar

A database-driven system for handling genomic sequences and screening genomic profiles.

mediamaker

The Blue Brain BioExplorer (BBBE) is a tool for data visualization experts and scientists to extract and analyze scientific data from visualization and interactive exploration

multisub

Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input directory and merges everything into a single output directory. Auto-detects input file formats. Can submit the results to multiple repositories from the command line.

python-outbreak-data

Python package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info