Reference mapping for single-cell genomics

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.

Oxbow makes genomic data ready for high-performance analytics.

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

𝒫robabilistic modeling of RNA velocity ⬱

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

`sdrf-pipelines` is the official SDRF file 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)

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"

Github repository for nanoSPLITS manuscript data and R scripts

DeepInsight3D package to deal with multi-omics or multi-layered data

Code for Highly Trustworthy Multimodal Learning (HTML) Method on Omics

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

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.