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.

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

Read specialized NGS formats as data frames in R, Python, and more.

𝒫robabilistic modeling of RNA velocity ⬱

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

A novel method for single-cell diagonal integration: scConfluence

SIMBA: SIngle-cell eMBedding Along with features

A repository to convert SDRF proteomics files into pipelines config files

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

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

Github repository for nanoSPLITS manuscript data and R scripts

Visual exploration of multi-dimensional proteomics data

Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data

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