There are 2 repositories under multiomics topic.
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.
The Proteomics Experimental Design file format: Standard for experimental design annotation
𝒫robabilistic modeling of RNA velocity ⬱
A repository to convert SDRF proteomics files into pipelines config files
SIMBA: SIngle-cell eMBedding Along with features
MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data
A novel method for single-cell diagonal integration: scConfluence
MOVIS: A Multi-Omics Software Solution for Multi-modal Time-Series Clustering, Embedding, and Visualizing Tasks, by Aleksandar Anžel, Dominik Heider, and Georges Hattab
DeepInsight3D package to deal with multi-omics or multi-layered data
Github repository for nanoSPLITS manuscript data and R scripts
Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data
It contains the functional code to analyze P2 scRNA-seq and scATAC-seq data.
This is a R package that intends to perform all the features possible by tensor decomposition based unsupervised feature extraction
R package for de novo pathway enrichment using KeyPathwayMiner
Regional Association of Methylation variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify Variable Methylated Regions (VMRs) in microarray DNA methylation data. Additionally, using Genotype (G) and Environmental (E) data, it can identify which G, E, G+E or GxE model better explains this variability.
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"
Project analyzing multi-omics genomics data from a COVID-19 study.
Bi-level regularized flux balance analysis of Synechococcus spp. PCC 7002
Multilayer Network analysis of medulloblastoma patients
Multi-omics Trustworthy Integration Framework (MoTIF)
ComplexHeatmap introduction
This repo is related to our benchmark entitled: "Decoding the microbiome-metabolome Nexus: A Systematic Benchmark of Integrative Strategies". We provide code to integrate metagenomics and metabolomics data to answer a variety of questions: such as global associations, data summarization, individual associations and feature selection.
Main Repository for my MASTER'S THESIS PROJECT
Free thoughts live
Identifying cancer-related signatures of endometrial and ovarian cancer to develop a reproductive cancer atlas.
Multi-omics differential expression and integration using PPI networks
A ShinyApp for visualization and explorering Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) data