Gene Expression Python Packages

enformer-pytorch

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

tf-bind-transformer

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

codontransformer

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

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

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.

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

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

modulector-sdk

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

pymrmr

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

cytocraft

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

vintools

Michael Vinyard's utilities

pinetree

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

ponyo

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

modulector

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

flashs

Spatially variable gene detection via frequency-domain kernel testing

ccbcge

A package to access gene expression data for breast cancer

chromoformer

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

orthomap

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

shapeshifter

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

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.