Multiomics Python Packages

oxbow

Oxbow makes genomic data ready for high-performance analytics.

sdrf-pipelines

SDRF official validator and converts SDRF to pipeline configuration files

diffbio

End-to-end differentiable bioinformatics for JAX/Flax NNX: soft Smith-Waterman alignment, read mapping and assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on the Avitai stack.

scarches

Reference mapping for single-cell genomics

mercat2

MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data

iptkl

A pythonic library for analysing immunopeptidomic experiments

garfield

Graph-based Contrastive Learning enable Fast Single-Cell Embedding

recon

Exploring multicellular coordination from single-cell gene expression / multi-omics using mutlilayer network representations

scmkl

Python package for single-cell analysis with multiple kernel learning.

cell-tools

Single-Cell Data Analysis Tools

sctrial

Trial-Aware Statistical Inference for Single-Cell Data

sc-tools

Single-Cell Data Analysis Tools