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.

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

ggca

Blazing fast Gene/GEM Correlation Analysis for Rust and Python

tangram-sc

Spatial alignment of single cell transcriptomic data.

anoexpress

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

pymrmr

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

z-zytome

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

cytocraft

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

vintools

Michael Vinyard's utilities

ponyo

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

ccbcge

A package to access gene expression data for breast cancer

chromoformer

Chromoformer - Pytorch

shapeshifter

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

stanmf

A python implementation of Stability NMF

flashs

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

expressionable

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

expressionable-cli

Transform, query, and merge tabular files with the expressionable command-line tool. 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

stochastic simulation of gene expression with site-specific translation rates

bio2bel-adeptus

Convert differential gene expression signatures for diseases from ADEPTUS to BEL

cimr

tool for continuously integrated meta-resource

ncountr

Python pipeline for Nanostring nCounter gene expression analysis — parse, QC, normalize, DE, pathway scoring