multi-omics

There are 14 repositories under multi-omics topic.

MOFA2
bioFAM / MOFA2
Multi-Omics Factor Analysis
multi-omics factor-analysis mofa
Language:R 278
scverse / muon
muon is a multimodal omics Python framework
multimodal-data multimodal-omics-analysis multi-omics anndata scanpy mudata muon scrna-seq scatac-seq cite-seq scverse
Language:Python 199
scverse / mudata
Multimodal Data (.h5mu) implementation for Python
anndata data-analysis genomics mudata multi-omics multimodal-omics-analysis muon scverse
Language:Python 68
RasmussenLab / MOVE
MOVE (Multi-Omics Variational autoEncoder) for integrating multi-omics data and identifying cross modal associations
associations-inference bayesian-inference integration multi-omics python variational variational-autoencoder variational-inference multi-modal
Language:Jupyter Notebook 59
BIMSBbioinfo / maui
Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
autoencoder bioinformatics cancer-genomics deep-learning latent-factor-model multi-omics
Language:Jupyter Notebook 49
zhangxiaoyu11 / OmiEmbed
Multi-task deep learning framework for multi-omics data analysis
multi-omics multi-task-learning deep-learning cancer
Language:Python 41
wukevin / babel
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
single-cell scrna-seq scatac-seq deep-neural-networks multi-omics
Language:Jupyter Notebook 37
biobakery / melonnpan
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
microbiome metabolomics metagenomics machine-learning public tools biobakery bioconductor metabolite-prediction multi-omics metabolite-compounds microbial-communities
Language:R 33
cantinilab / Mowgli
Single-cell multi-omics integration using Optimal Transport
dictionary-learning matrix-factorization multi-omics multi-omics-integration optimal-transport single-cell
Language:Python 33
JonnyTran / OpenOmics
A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.
genomics multi-omics data-integration python data-manipulation
Language:Python 29
selbouhaddani / OmicsPLS
R package for High dimensional data analysis and integration with O2PLS!
bioinformatics biostatistics omics multi-omics data-integration principal-component-analysis pca partial-least-squares-regression pls latent-variable-models
Language:R 29
scverse / Muon.jl
Muon for Julia
omics multi-omics single-cell muon anndata mudata scverse julia
Language:Julia 25
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"
multi-omics binder-ready integrative-omics omics omics-data-integration papers-with-code
Language:Jupyter Notebook 24
abodein / timeOmics
Time-Course Multi-Omics data integration
cluster integration multi-omics time-series
Language:R 23
PMBio / MuDataSeurat
.h5mu files interface for Seurat
seurat multimodal-omics multi-omics scrna-seq anndata mudata
Language:R 20
OmicsSuite / OmicsSuite.github.io
OmicsSuite website for releasing new version.
bioinformatics genomics java javafx metabolomics multi-omics omicssuite singlecell software transcriptomics
Language:HTML 19
pievos101 / GNN-SubNet
Disease subnetwork detection with explainable Graph Neural Networks
explainable-ai graph-neural-networks disease-networks multi-omics
Language:Python 19
epruesse / ymp
Flexible omics pipeline
omics-pipeline conda-environment ymp metagenomics rna-seq pipeline snakemake extensible multi-omics bioinformatics hacktoberfest hacktoberfest-accepted hacktoberfest2022
Language:Python 18
ashleymaeconard / TIMEOR
TIMEOR: Trajectory Inference and Mechanism Exploration with Omics Data in R
analysis factor-binding gene-regulatory-networks multi-omics r rshinyapp time-series transcription-factor website
Language:R 17
glasgowcompbio / pyMultiOmics
Python toolbox for multi-omics data mapping and analysis
multi-omics data-integration bioinformatics machine-learning transcriptomics proteomics metabolomics
Language:Jupyter Notebook 17
drug-disease-profile-matching
krassowski / drug-disease-profile-matching
Multi-omics disease sub-type specific drug repositioning aided with expression signatures from ConnectivityMap
drug-discovery drug-repurposing stratification multi-omics lincs gct l1000
Language:Jupyter Notebook 16
bacnet
becavin-lab / bacnet
BACNET is a Java based platform to develop website for multi-omics analysis
bacnet genomics data-visualization transcriptomics proteomics listeria multi-omics website bioinformatics
Language:Java 13
HuMMuS
cantinilab / HuMMuS
Molecular interactions inference from single-cell multi-omics data
biological-networks epigenomics multi-omics multilayer-networks single-cell transcriptomics
Language:Python 13
LamineTourelab / MOGONET
MOGONET (Multi-Omics Graph cOnvolutional NETworks) is multi-omics data integrative analysis framework for classification tasks in biomedical applications.
deep-learning graph-convolutional-networks machine-learning pytorch multi-omics multi-omics-integration multimodal-deep-learning mogonet
Language:Python 12
himelmallick / IntegratedLearner
Integrated Machine Learning for Multi-omics Classification and Prediction
machine-learning multi-omics bayesian metagenomics metabolomics multiple-covariates repeated-measures
Language:HTML 11
scverse / muon-tutorials
Tutorials for multimodal omics data analysis
multi-omics single-cell mudata muon scverse
Language:Jupyter Notebook 11
chenweng1991 / redeemR
R package for ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling.
cell-state clonal-analysis lineage-tracing multi-omics single-cell single-cell-genomics
Language:Jupyter Notebook 9
ocbe-uio / survomics
Tutorial on survival modeling with omics data
multi-omics survival-analysis tutorial bayesian-cox-models penalized-cox-models survival-model-evaluation
Language:TeX 9
garimasingh128 / Ovarian-Cancer-Subtypes-Identification
🧠Deep Learning-based✔️ Ovarian Cancer🙅🏻‍♀️ Subtypes Identification using Multi-Omics Data✅
biodata biodatamining ovarian-cancer deep-learning multi-omics
Language:Jupyter Notebook 8
MoTrPAC / MotrpacRatTraining6mo
Analysis of the MoTrPAC endurance exercise training study in 6-month-old rats
data-analysis data-visualization multi-omics r
Language:R 8
Shamir-Lab / INTEND
INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation datasets covering disjoint sets of samples
machine-learning-algorithms multi-omic-integration multi-omics
Language:R 8
CBIGR / SUBATOMIC
The SUbgraph BAsed mulTI-OMIcs Clustering (SUBATOMIC) framework infers interpretable modules with a specific topology.
bioinformatics bioinformatics-pipeline multi-omics networks modules network-analysis
Language:Python 7
jguhlin / ODG
ODG: Omics Database Generator - Integration toolkit for -omics data
database database-generator graph-database genomics bioinformatics multi-omics genome-annotation omics-database-generator
Language:Clojure 7
acabassi / coca
R package for COCA: Cluster-of-Clusters Analysis
cluster-analysis cluster-of-clusters clustering coca genomics integrative-clustering multi-omics
Language:R 6
Shamir-Lab / MONET
MONET
multi-omics clustering graph-algorithms
Language:R 6
maxsonBraunLab / CITEViz
CITEViz: Replicating the Interactive Flow Cytometry Workflow in CITE-Seq
flow-cytometry multi-omics r-shiny scrna-seq single-cell
Language:R 5