Genomic Data Analysis Python Packages

gcmapexplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:

annsql

A Python SQL tool for converting Anndata objects to a relational DuckDb database. Methods are included for querying and basic single-cell preprocessing (experimental).

airpg

Accessing the inverted repeats of archived plastid genomes

gppy

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

genomap

Genomap converts tabular gene expression data into spatially meaningful images.

phigaro

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

selene-sdk

a framework for training sequence-level deep learning networks

helen

RNN based assembly HELEN. It works paired with MarginPolish.

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

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

omacase

a tool to analyze optical mapping data, with _de novo_ repeat motif detection and analysis capabilities