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

scarches

Reference mapping for single-cell genomics

iptkl

A pythonic library for analysing immunopeptidomic experiments

diffbio

End-to-end differentiable bioinformatics pipelines built on JAX/Flax NNX

scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

garfield

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

mercat2

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

ddipy

Python client for OmicsDI Restful API

scmkl

Single-cell analysis using Multiple Kernel Learning

cell-tools

cell_tools - Analysis Tools for Single-Cell Data

pyddi-xupan

web-service client of omicsDI API

sc-tools

sc-tools - Analysis Tools for Single-Cell Data

scarf-toolkit

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.