multiomics

Combined RNA and ATAC Footprint Training of Gene Regulatory Network

Reference mapping for single-cell genomics

Oxbow makes genomic data ready for high-performance analytics.

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

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.

𝒫robabilistic modeling of RNA velocity ⬱

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

SDRF official validator and converts SDRF to pipeline configuration files

A novel method for single-cell diagonal integration: scConfluence

Precision Medicine MCP Platform: A set of bioinformatics servers + tools - production multiomics/genomics + spatial transcriptomics. Examples for ovarian cancer, breast cancer and preventative cardiovascular conditions

The simplest, fastest software for studying gene regulation in single-cell data. Core SCENIC and SCENIC+ rewritten in Rust, with a Python API. Built and scaled with the Huang Lab at Mount Sinai.

SIMBA: SIngle-cell eMBedding Along with features

Plain-language guide to causal inference for microbiome & multi-omics: DAGs/backdoor, confounders vs mediators/colliders, causal mediation (ACME/ADE/Total), and Double Machine Learning (DML) with toy examples + code.

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

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

Regional Association of DNA Methylome variability with the Exposome and geNome (RAMEN) is an R package which goal is to identify Variable Methylated Loci (VML) in microarray DNA methylation data. Then, using genome (G) and exposome (E) data, it can identify which individual (G or E) or joint (G+E or GxE) model better explains the VML 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"

Exploring multicellular coordination from single-cell gene expression / multi-omics using mutlilayer network representations

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.

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