Gene Expression Python Packages

enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

ggca

Blazing fast Gene/GEM Correlation Analysis for Rust and Python

helical

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

codontransformer

CodonTransformer (2M+ Downloads); The tool for codon optimization, optimizing DNA for protein expression

tf-bind-transformer

A repository with exploration into using transformers to predict DNA ↔ transcription factor binding

tangram-sc

Spatial alignment of single cell transcriptomic data.

dracoonpy

DRaCOoN: data-driven differential co-expression and differential regulatory network inference from transcriptomics data across two conditions (BMC Bioinformatics 2025)

nichenetpy

nichenetpy: the python implementation of the NicheNet method. The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.

anoexpress

Anopheles gene expression in insecticide resistance

z-zytome

Zytome is declarative library for handling gene expression data for various data portals or datasets.

flashs

Spatially variable gene detection via frequency-domain kernel testing

pymrmr

Python3 binding to mRMR Feature Selection algorithm (currently not maintained)

scunveil

Pretrained scRNA-seq toolkit for generating cell embeddings and depth-enriched gene expression directly from raw UMI counts.

cytocraft

The Cytocraft package provides 3D reconstruction of spatial configuration of transcription centers

ponyo

Software to simulate compendium-wide gene expression data using a VAE.

cytorete

Cell-type-resolved gene regulatory network inference from single-cell data.

vintools

Michael Vinyard's utilities

deepspotm

Multimodal foundation model predicting transcriptome-wide virtual spatial transcriptomics from histology.

modulector-sdk

An open platform which provides information about miRNAs and genes from different popular databases

chromoformer

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

shapeshifter

Transform, query, and merge tabular files with the expressionable Python module. This tool is used primarily for gene-expression data.

shapeshifter-cli

Transform, query, and merge tabular files with the expressionable command-line tool. This tool is used primarily for gene-expression data.

pinetree

🌲 a flexible gene expression simulator with codon-specific translation rates

bioapi-sdk

A powerful abstraction of gene databases