Reference mapping for single-cell genomics

Oxbow makes genomic data ready for high-performance analytics.

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.

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

SIMBA: SIngle-cell eMBedding Along with features

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

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.

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

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

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

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"

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.

Github repository for nanoSPLITS manuscript data and R scripts

An R package to perform differential network analysis in single and multi-omic data. It can also be used for feature selection in ML.

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