multiomics

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.

bioinformatics big-data genomics clustering scrna-seq graph-analytics memory-efficient tsne differential-expression umap dimension-reduction single-cell-genomics single-cell-rna-seq scalable-data-analysis single-cell-atac-seq multiomics cite-seq pseudotime scatac-seq gene-modules

UpdatedNov 19, 2025
Python

bigbio /proteomics-sample-metadata

Star101

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets

metadata proteomics proteomics-datasets multiomics proteomexchange sdrf pride-metadata msrun-metadata sdrf-proteomics proteomics-community proteomics-experiments mage-tab

UpdatedFeb 20, 2026
HTML

Intuitive guide to multi-omics integration with toy examples: supervised latent components (DIABLO), unsupervised shared/partial/unique structure (DIVAS), VAEs/conditional VAEs, and key baselines (MOFA, JIVE, SNF) with practical tips + code.

machine-learning bioinformatics data-integration diablo microbiome latent-variables variational-autoencoder multiomics

UpdatedDec 28, 2025
Python

pyrovelocity /pyrovelocity

Star49

𝒫robabilistic modeling of RNA velocity ⬱

probabilistic-programming transcriptomics pyro probabilistic-models single-cell-genomics single-cell-rna-seq rna-velocity-estimation multiomics deep-generative-model developmental-trajectories rna-velocity rna-splicing single-cell-multiomics cell-fate-determination rna-splicing-analysis

UpdatedFeb 16, 2026
Python

CostaLab /scMEGA

Star44

scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference

single-cell grn multiomics

UpdatedSep 20, 2024
R

bigbio /sdrf-pipelines

Star29

`sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files

proteomics mass-spectrometry openms maxquant msstats multiomics sdrf proteomics-data-analysis

UpdatedFeb 5, 2026
Python

cantinilab /scconfluence

Star26

A novel method for single-cell diagonal integration: scConfluence

integration single-cell dimension-reduction optimal-transport multiomics

UpdatedNov 3, 2025
Python

huidongchen /simba

Star20

SIMBA: SIngle-cell eMBedding Along with features

graph dimensionality-reduction embedding graph-embedding single-cell-analysis multiomics

UpdatedJan 6, 2026
Python

futianfan /GenoCraft

Star19

GenoCraft: A Comprehensive, User-Friendly Web Platform for High-Throughput Omics Data Analysis and Visualization (https://arxiv.org/pdf/2312.14249)

visualization flask rna-seq genomics ngs next-generation-sequencing protein omics single-cell pathway-analysis omics-data-integration bulk-rna-seq multiomics

UpdatedMay 28, 2025
SCSS

raw-lab /mercat2

Star13

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

python diversity plotly protein dask fastq k-mer-counting k-mer-frequency divideandconquer metagenomic-analysis metatranscriptomic-analysis kmer-frequency-count nucleotides diversity-estimation database-independent-analysis multiomics multiomics-data

UpdatedJan 28, 2026
HTML

AAnzel /MOVIS

Star10

MOVIS: A Multi-Omics Software Solution for Multi-modal Time-Series Clustering, Embedding, and Visualizing Tasks, by Aleksandar Anžel, Dominik Heider, and Georges Hattab

visualization machine-learning bioinformatics time-series cross-platform clustering web-app exploratory-data-analysis time-series-analysis multiomics multiomics-data

UpdatedMay 17, 2022
Python

Cajun-data /nanoSPLITS

Star10

Github repository for nanoSPLITS manuscript data and R scripts

proteomics proteomics-data single-cell-omics multiomics

UpdatedOct 11, 2024
HTML

lynnlangit /precision-medicine-mcp

Star10

Precision Medicine MCP Platform: 15 bioinformatics servers (80+ tools) - production multiomics/genomics + spatial transcriptomics. Example and demo for ovarian cancer

bioinformatics transcriptomics precision-medicine multiomics agentic-ai

UpdatedFeb 20, 2026
Python

prokischlab /omicsDiagnostics

Star9

This repository contains different scripts to automate and visualize analysis performed for the "Integration of proteomics with genomics and transcriptomics increases the diagnosis rate of Mendelian disorders"

rna-seq diagnostics outlier-detection proteomics hpo multiomics rare-disease

UpdatedJun 4, 2025
R

davidenoma /moka

Star8

MOKA Snakemake pipeline for GWAS incorporating user provided multi-omics data sources such as gene expression, neural network weights, transcription factor binding, and evolutionary conservation scores.

python snakemake r kernel multiomics genome-wide-association-studies