Ursgal - universal Python module combining common bottom-up proteomics tools for large-scale analysis

🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

scDataset: Scalable Data Loading for Deep Learning on Large-Scale Single-Cell Omics

Enzyme-constrained genome-scale models in python

A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)

Framework for efficient high-dimensional association analyses.

Signaling Pathway Reconstruction Analysis Streamliner (SPRAS)

PyIOmica (pyiomica) is a Python package for omics analyses.

A spatially explicit trait- and individual-based microbial systems modelling framework

A repository for hosting Nextflow DSL2 module files containing tool-specific process definitions and their associated documentation for MSKCC

A simple python package for doublet detection in scRNA-seq data

Comparative Metatranscriptomics Workflow

A simple python package for doublet detection in scRNA-seq data. This repo is read-only, please visit GCS-ZHN/socube to submit issue and PR.

a python library providing data processing and machine learning tools for computational omics, with emphasis on explainability

OMD Curation Toolkit is a python package designed for the download and curation of metadata and fastq files of public omics datasets.

Utils for loading HuBMAP data formats

FUNctional analysis worKflows Interface

Reusable in-situ sequencing analysis workflow orchestrated by Nextflow

Python package for creating interactive and static visualizations of multi-omics data

A bioinformatics extension of 🤗 Datasets library, built for ML applications on biological and omics data, offering easy integration of metadata and low-code data management tools.