Projects in Awesome Lists tagged with omics

https://github.com/Starlitnightly/omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

bioinformatics bulk-rna-seq omics single-cell

Last synced: 16 Mar 2025

https://github.com/bigomics/omicsplayground

Visual self-service analytics platform for big omics data.

genomics genomics-visualization omics rna-seq rna-seq-analysis

Last synced: 25 Feb 2026

https://github.com/rajewsky-lab/openst

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

bioinformatics omics spatial-transcriptomics transcriptomics

Last synced: 02 Feb 2026

https://github.com/pachterlab/voyager

From geospatial to spatial -omics

bioconductor eda esda exploratory-data-analysis omics r r-package rstats spatial spatial-statistics spatial-transcriptomics transcriptomics

Last synced: 10 Apr 2025

https://github.com/jpquast/protti

Picotti lab data analysis package.

data-analysis lip-ms mass-spectrometry omics protein proteomics r systems-biology

Last synced: 16 Jan 2026

https://github.com/biocore/gneiss

compositional data analysis toolbox

balance compositional-statistics omics tree

Last synced: 09 Apr 2025

https://github.com/ursgal/ursgal

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

mass-spectrometry ms-data mzml omics peptide-identification proteomics proteomics-data python

Last synced: 30 Apr 2025

https://github.com/camlab-bioml/rakaia

Scale interactive spatial omics in the browser to thousands of images | https://rakaia.io/

browser histology imaging-mass-cytometry multiplexed-imaging omics spatial-analysis spatial-biology spatial-data spatial-proteomics spatial-transcriptomics viewer visium xenium zarr

Last synced: 08 Mar 2026

https://github.com/shenwanxiang/bidd-aggmap

Jigsaw-like AggMap: A Robust and Explainable Multi-Channel Omics Deep Learning Tool

ai clustering deep-learning machine-learning omics visualization

Last synced: 16 Jan 2026

https://github.com/cafferychen777/microbiomestat

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

16s-rrna amplicon-sequencing dada2 longitudinal-data metagenomes metagenomic-analysis microbiome microbiome-analysis microbiome-data microbiome-workflow omics omics-data-integration phyloseq qiime2 statistics visualization

Last synced: 16 Apr 2025

https://github.com/abbvie-external/OmicNavigator

Open-Source Software for Omic Data Analysis and Visualization

bioinformatics genomics omics opencpu r

Last synced: 28 Sep 2025

https://github.com/selbouhaddani/OmicsPLS

R package for High dimensional data analysis and integration with O2PLS!

bioinformatics biostatistics data-integration latent-variable-models multi-omics omics partial-least-squares-regression pca pls principal-component-analysis

Last synced: 13 Apr 2025

https://github.com/scdataset/scdataset

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

big-data bioinformatics deep-learning machine-learning omics pytorch rna-seq single-cell

Last synced: 08 Oct 2025

https://github.com/scverse/muon.jl

Muon for Julia

anndata julia mudata multi-omics muon omics scverse single-cell

Last synced: 12 Oct 2025

https://github.com/geniusrise/awesome-healthcare-datasets

Healthcare and biomedical datasets, for AI/ML

awesome-list biomedical clinical datasets healthcare imaging omics

Last synced: 16 Jan 2026

https://github.com/krassowski/multi-omics-state-of-the-field

Analyses for "State of the field in multi-omics research: from computational needs to data mining and sharing"

binder-ready integrative-omics multi-omics omics omics-data-integration papers-with-code

Last synced: 13 Apr 2025

https://github.com/ginkgobioworks/geckopy

Enzyme-constrained genome-scale models in python

data-integration enzyme-constraints kinetics omics proteomics systems-biology thermodynamics

Last synced: 25 Oct 2025

https://github.com/the-omics-os/lobster

The self-evolving agentic framework for bioinformatics

agents bioinformatics langgraph lobster omics proteomics transcriptomics

Last synced: 25 Apr 2026

https://github.com/futianfan/genocraft

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

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

Last synced: 12 Oct 2025

https://github.com/cran-task-views/omics

CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

cran genomics metabolomics omics proteomics r rstats task-views transcriptomics

Last synced: 13 Apr 2025

https://github.com/transbiozi/biomm

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

biomm dna-methylation elasticnetregression epigenomics gene-expression genomics go-pathway gwas high-dimensional kegg-pathway machine-learning omics phenotype-prediction random-forest svm transcriptomics

Last synced: 24 Feb 2026

https://github.com/delosh653/echo

An application to find and visualize circadian rhythms in time course data using extended harmonic oscillators.

bioinformatics bioinformatics-tool circadian circadian-rhythm circadian-rhythmicity echo extended-harmonic-oscillators finding-rhythms omics oscillators proteomics transcriptomics

Last synced: 11 Apr 2025

https://github.com/traincheckai/mojomics

Supercharging bioinformaticians with🔥

mojo omics

Last synced: 10 May 2025

https://github.com/thegreatherrlebert/rustims

A Framework for IMS-MS Raw Data Processing written in Rust and Python.

bottom-up data-independent-acquisition high-throughput ion-mobility-spectrometry mass-spectrometry omics proteomics pyo3 python raw-data rust-lang timstof

Last synced: 16 May 2025

https://github.com/fgcz/bfabricshiny

Manage life sciences data using R and b-fabric - a WSDL/REST interface and a tool box; main focus on MS data

bfabric experiments mass-spectrometry omics shiny wsdl

Last synced: 14 Aug 2025

https://github.com/guokai8/o2plsda

Omics data integration with o2plsda

integration multi-omics o2pls omics plsda

Last synced: 02 Apr 2026

https://github.com/perrin-isir/xomx

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

bioinformatics computational-biology explainability machine-learning omics

Last synced: 18 Jan 2026

https://github.com/biomedsciai/geno4sd

An python omics data toolkit for the analysis across biological scales

cancer-genomics dna machine-learning omics omics-data population-genetics population-genomics

Last synced: 28 Jul 2025

https://github.com/vitessce/vitessce-data

Utils for loading HuBMAP data formats

gehlenborglab hidivelab hubmap imaging kharchenkolab omics single-cell spatial vitessce

Last synced: 08 Apr 2025

https://github.com/medomicslab/medomics

ai data-analysis data-modeling data-science data-visualization electron golang heterogeneous-data machine-learning medical-informatics nodejs omics python react

Last synced: 11 Apr 2026

https://github.com/marmarelis/qdiffusion.jl

Leveraging the full dimensionality of single-cell transcriptomics (among other things!)

embeddings estimation high-dimensional-statistics latent-variable-models omics

Last synced: 03 Feb 2026

https://github.com/broadinstitute/celligner2

A new version of the celligner package using VAEs. Inspired from the Theis lab's scArches.

alignment cancer-genomics machine-learning omics rna-seq vae-pytorch

Last synced: 11 Mar 2026

https://github.com/luk3d/hivy.space

🚀 Welcome to Hivy Space, the home for All Anime, Animation, Comic and Manga Lovers

anime anime-list anime-search anime-website animes comic community gallery hivy hivyspace manga omics social-network

Last synced: 08 Jul 2025

https://github.com/fjcamlab/deco

DECO :: Decomposing heterogeneous population cohorts for patient stratification and discovery of biomarkers using omic data profiling. R package

bioinformatics deco differential-expression heterogeneity heterogeneous-populations omic-data-profiling omics patients-stratification r sampling-methods stratification

Last synced: 19 Feb 2026

https://github.com/nshen7/decemedip

An R package for deconvoluting cell types in bulk-tissue/cell-free MeDIP-seq data leveraging a Bayesian hierarchical model. Depends on RStan.

bayesian bayesian-data-analysis bayesian-inference bioinformatics dna-methylation dna-methylation-data epigenomics generative-model omics rstan stan

Last synced: 26 Jan 2026

https://github.com/berenslab/sbnn

A sparse bottleneck neural network to predict electrophysiological properties of neurons from their gene expression.

bottleneck electrophysiology lasso machine-learning neural-networks omics sparse visualization

Last synced: 01 Feb 2026

https://github.com/saezlab/funki

FUNctional analysis worKflows Interface

analysis omics python workflow

Last synced: 14 Apr 2025

https://github.com/cafferychen777/microbiomestat-turtorial-professional-version

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.

16s 16s-rrna 16s-seq analysis data-analysis metagenomes metagenomic-analysis metagenomic-pipeline metagenomics microbiome microbiome-analysis microbiome-analysis-pipelines microbiome-data microbiome-workflow omics omics-data omics-data-analysis omics-data-integration visualization

Last synced: 03 Jan 2026

https://github.com/psmyth94/biosets

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.

big-data bioinfo classification data-preprocessing data-processing data-science datasets genomics high-performance huggingface machine-learning metadata omics open-source pandas polars proteomics pyarrow python regression

Last synced: 20 Jan 2026

https://github.com/a-r-j/tb-resources

List of online databases and resources for Mycobacterium Tuberculosis

computational-biology curated drug-discovery genomics genomics-data genomics-data-sets integration list mycobacterium mycobacterium-tuberculosis omics proteomics proteomics-data proteomics-data-integration proteomics-datasets transcriptomics transcriptomics-data transcriptomics-data-integration transcriptomics-datasets tuberculosis

Last synced: 18 Mar 2026

https://github.com/raivivek/convert-this-to-that

Quickly lookup how to convert common bioinformatics file formats

bioinformatics genomics ngs omics

Last synced: 06 Jun 2026

https://github.com/umr1283/CARoT

Centralised and Automated RepOrting Tools

omics quality-control r r-package r-stats reporting

Last synced: 30 Jul 2025

https://github.com/sdsc-ordes/modos-api

Python API to manage multi-omics digital objects

cli fair metadata multi-omics omics rest-api

Last synced: 08 Feb 2026

https://github.com/sdsc-ordes/modos-poster

Poster presentation of modos

omics poster presentation

Last synced: 26 Jan 2026

https://github.com/ayushnoori/datalens

Open data analysis platform for Alzheimer's disease. Created for CS50 at Harvard College.

alzheimer cs50 omics

Last synced: 17 Feb 2026

https://github.com/slipnitskaya/regulas

regulAS: Bioinformatics Toolset for ML-assisted Integrative Analysis of Alternative Splicing Regulome using RNA-Seq data

bioinformatics explainable-ml feature-selection machine-learning omics rna-seq software splicing transcriptomics

Last synced: 20 Apr 2026

https://github.com/hyletic/lovdtools

A fluent API client for querying the Global Variome shared LOVD instance.

api-client api-client-python bioinformatics bioinformatics-tool data-acquisition data-science fluent-interface genomics lovd multiomics omics

Last synced: 14 Jan 2026

https://github.com/multiomics-analytics-group/acore

Functionality to preprocess and analyse multi-omics data

analysis omics omics-data-integration preprocessing-data

Last synced: 23 Jan 2026

https://github.com/biosustain/omics_valid

Specifications and validators for omics data formats used on C. autoethanogemum C1 program

bioinformatics biology omics parser

Last synced: 09 May 2026

https://github.com/jmw86069/jamma

Jam MA-plots, volcano plots, other relevant genomics visualizations

data-quality ma-plots omics visualization

Last synced: 23 May 2026

https://github.com/tacular-omics/psimodpy

Python library for parsing and querying the PSIMOD post-translational modification (PTM) controlled vocabulary.

omics ontology peptide protein proteomics psi ptm

Last synced: 05 May 2026

https://github.com/kechrislab/kechrislab.github.io

Kechris Homepage

bioinformatics biostatistics colorado home homepage informatics katerina kechris lab omics page phd professor research site software university website

Last synced: 26 Feb 2026

https://github.com/sdsc-ordes/modos-schema

Metadata schema for the SMOC Multi-Omics Digital-Object

omics ontology

Last synced: 27 Feb 2026

https://github.com/tacular-omics/unimodpy

Python library for parsing and querying the UNIMOD post-translational modification (PTM) controlled vocabulary.

omics ontology peptide protein proteomics psi ptm unimod

Last synced: 05 May 2026

https://github.com/tacular-omics/uniprotptmpy

Python library for parsing and querying the UniProt post-translational modification (PTM) controlled vocabulary.

omics ontology peptide protein proteomics ptm uniprot

Last synced: 05 May 2026

https://github.com/abikesa/aging

Aging

agility frailty independence memory omics sensory

Last synced: 25 Mar 2025

https://github.com/cumbof/open-omics-api

A open-source framework for organising multi-omics data from heterogeneous data sources

api data-integration data-management genomics mongodb omics

Last synced: 20 Jul 2025

https://github.com/kevinrue/xaringan_nextgen_omics_2021

Slides for: NextGen Omics UK, 4-5 November 2021

hacktoberfest nextgen omics single-cell

Last synced: 17 Feb 2026

https://github.com/goncalojustino/maxquant-windows-scheduler

A lightweight PowerShell 7 scheduler for running multiple MaxQuant jobs in parallel on Windows, using a queue-based submission model, CPU affinity, and robust success/failure classification.

bioinformatics computational-proteomics mass-spectrometry maxquant omics powershell proteomics scheduler windows workflow