Gene Expression Python Packages

enformer-pytorch

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

helical

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

ggca

Blazing fast Gene/GEM Correlation Analysis for Rust and Python

codontransformer

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

tf-bind-transformer

Transformer for Transcription Factor Binding

tangram-sc

Spatial alignment of single cell transcriptomic data.

z-zytome

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

pymrmr

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

anoexpress

A package to access insecticide resistance gene expression meta analyse in Anopheles mosquitoes

vintools

Michael Vinyard's utilities

cytocraft

The Cytocraft package provides prediction of chromosome configuration based on subcellular resolution spatial transcriptomics.

ponyo

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

shapeshifter

A tool for managing large datasets

stanmf

A python implementation of Stability NMF

ccbcge

Python package to access Breast Cancer Gene Expression data

chromoformer

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

flashs

Flash-S: Frequency-domain Linearized Adaptive Spatial Hypothesis testing via Sketching

pinetree

stochastic simulation of gene expression with site-specific translation rates

shapeshifter-cli

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

expressionable

A tool for managing large datasets

sobolev-alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

expressionable-cli

A command-line tool for transforming large data sets

bio2bel-adeptus

Convert differential gene expression signatures for diseases from ADEPTUS to BEL

ncountr

Python pipeline for Nanostring nCounter data analysis