Genomic Data Analysis Python Packages

annsql

The AnnSQL package enables SQL based queries on AnnData objects.

gcmapexplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:

airpg

A package to automatically access the inverted repeats of archived plastid genomes

phigaro

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

helen

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

genomap

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

selene-sdk

a framework for training sequence-level deep learning networks

gene2tab

Creates a table with the presence/absence of genes in samples

gppy

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

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