Genomic Data Analysis Python Packages

scholion

Your genome, labs, prescriptions and wearables sit in silos that never compare notes, so contradictions go unnoticed. This reads them against each other, with the source behind every answer — one local engine behind a web UI, a CLI, a Claude skill, and an Ouroboros plugin.

annsql

The AnnSQL package enables SQL based queries on AnnData objects.

gcmapexplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:

airpg

Accessing the inverted repeats of archived plastid genomes

selene-sdk

a framework for training sequence-level deep learning networks

phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages

genomap

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)

helen

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

gppy

[G]enomic [P]ositioning with [Py]thon

gene2tab

This script is used to convert the output of ABRICATE tabulated output into a matrix samples with the genes as columns and the presence/absence of the gene as the values.

firecaller

FIREcaller: Python library for detecting Frequently Interacting REgions (FIREs) from Hi-C data

omacase

an open-source (GPLv3) standalone Python package to analyze optical mapping data, with de novo repeat motif detection and analysis capabilities