multi-omics

There are 14 repositories under multi-omics topic.

MOFA2
bioFAM / MOFA2
Multi-Omics Factor Analysis
factor-analysis mofa multi-omics
Language:R 304
scverse / muon
muon is a multimodal omics Python framework
anndata cite-seq mudata multi-omics multimodal-data multimodal-omics-analysis muon scanpy scatac-seq scrna-seq scverse
Language:Python 216
scverse / mudata
Multimodal Data (.h5mu) implementation for Python
anndata data-analysis genomics mudata multi-omics multimodal-omics-analysis muon scverse
Language:Python 77
RasmussenLab / MOVE
MOVE (Multi-Omics Variational autoEncoder) for integrating multi-omics data and identifying cross modal associations
associations-inference bayesian-inference integration multi-modal multi-omics python variational variational-autoencoder variational-inference
Language:Jupyter Notebook 64
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 48
zhangxiaoyu11 / OmiEmbed
Multi-task deep learning framework for multi-omics data analysis
multi-omics multi-task-learning deep-learning cancer
Language:Python 39
wukevin / babel
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
deep-neural-networks multi-omics scatac-seq scrna-seq single-cell
Language:Jupyter Notebook 38
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 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 34
JonnyTran / OpenOmics
A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.
data-integration data-manipulation genomics multi-omics python
Language:Python 31
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 31
scverse / Muon.jl
Muon for Julia
anndata julia mudata multi-omics muon omics scverse single-cell
Language:Julia 27
PMBio / MuDataSeurat
.h5mu files interface for Seurat
anndata mudata multi-omics multimodal-omics scrna-seq seurat
Language:R 26
abodein / timeOmics
Time-Course Multi-Omics data integration
cluster integration multi-omics time-series
Language:R 24
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
HuMMuS
cantinilab / HuMMuS
Molecular interactions inference from single-cell multi-omics data
biological-networks epigenomics multi-omics multilayer-networks single-cell transcriptomics
Language:R 22
pievos101 / GNN-SubNet
Disease subnetwork detection with explainable Graph Neural Networks
disease-networks explainable-ai graph-neural-networks multi-omics
Language:Python 21
glasgowcompbio / pyMultiOmics
Python toolbox for multi-omics data mapping and analysis
multi-omics data-integration bioinformatics machine-learning transcriptomics proteomics metabolomics
Language:Jupyter Notebook 19
epruesse / ymp
Flexible omics pipeline
bioinformatics conda-environment extensible hacktoberfest hacktoberfest-accepted hacktoberfest2022 metagenomics multi-omics omics-pipeline pipeline rna-seq snakemake ymp
Language:Python 18
himelmallick / IntegratedLearner
Integrated Machine Learning for Multi-omics Classification and Prediction
bayesian machine-learning metabolomics metagenomics multi-omics multiple-covariates repeated-measures
Language:HTML 18
OmicsSuite / OmicsSuite.github.io
OmicsSuite website for releasing new version.
bioinformatics genomics java javafx metabolomics multi-omics omicssuite singlecell software transcriptomics
Language:HTML 18
ashleymaeconard / TIMEOR
TIMEOR: Trajectory Inference and Mechanism Exploration with Omics Data in R
transcription-factor time-series gene-regulatory-networks website r rshinyapp multi-omics factor-binding analysis
Language:R 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 bioinformatics data-visualization genomics listeria multi-omics proteomics transcriptomics website
Language:Java 13
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 12
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 mogonet multi-omics multi-omics-integration multimodal-deep-learning pytorch
Language:Python 12
scverse / muon-tutorials
Tutorials for multimodal omics data analysis
multi-omics single-cell mudata muon scverse
Language:Jupyter Notebook 12
ocbe-uio / survomics
Tutorial on survival modeling with omics data
bayesian-cox-models mlr3 mlr3proba multi-omics penalized-cox-models survival-analysis survival-model-evaluation tutorial
Language:TeX 11
garimasingh128 / Ovarian-Cancer-Subtypes-Identification
🧠Deep Learning-based✔️ Ovarian Cancer🙅🏻‍♀️ Subtypes Identification using Multi-Omics Data✅
biodata biodatamining deep-learning multi-omics ovarian-cancer
Language:Jupyter Notebook 8
jguhlin / ODG
ODG: Omics Database Generator - Integration toolkit for -omics data
bioinformatics database database-generator genome-annotation genomics graph-database multi-omics omics-database-generator
Language:Clojure 8
MoTrPAC / MotrpacRatTraining6mo
Analysis of the MoTrPAC endurance exercise training study in 6-month-old rats
r data-analysis data-visualization multi-omics
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
maxsonBraunLab / CITEViz
CITEViz: Replicating the Interactive Flow Cytometry Workflow in CITE-Seq
flow-cytometry multi-omics r-shiny scrna-seq single-cell
Language:R 6
nf-core / hicar
Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
nf-core nextflow workflow pipeline hicar hic atac atac-seq transcriptome multi-omics
Language:Nextflow 6
rachelgriffard / optima
An open-source R package for the Tapestri platform for integrative single cell multiomics data analysis
multi-omics omics single-cell single-cell-analysis mission-bio tapestri
Language:HTML 6

multi-omics

bioFAM / MOFA2

scverse / muon

scverse / mudata

RasmussenLab / MOVE

BIMSBbioinfo / maui

zhangxiaoyu11 / OmiEmbed

wukevin / babel

cantinilab / Mowgli

biobakery / melonnpan

JonnyTran / OpenOmics

selbouhaddani / OmicsPLS

scverse / Muon.jl

PMBio / MuDataSeurat

abodein / timeOmics

krassowski / multi-omics-state-of-the-field

cantinilab / HuMMuS

pievos101 / GNN-SubNet

glasgowcompbio / pyMultiOmics

epruesse / ymp

himelmallick / IntegratedLearner

OmicsSuite / OmicsSuite.github.io

ashleymaeconard / TIMEOR

krassowski / drug-disease-profile-matching

becavin-lab / bacnet

chenweng1991 / redeemR

LamineTourelab / MOGONET

scverse / muon-tutorials

ocbe-uio / survomics

garimasingh128 / Ovarian-Cancer-Subtypes-Identification

jguhlin / ODG

MoTrPAC / MotrpacRatTraining6mo

Shamir-Lab / INTEND

CBIGR / SUBATOMIC

maxsonBraunLab / CITEViz

nf-core / hicar

rachelgriffard / optima