Fast, sensitive and accurate integration of single-cell data with Harmony

NicheNet: predict active ligand-target links between interacting cells

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis

ADTnorm normalizes the cell surface protein measurement of CITE-seq data, facilitating across batches and across studies data integration.

Some of the projects i made when starting to learn R for Data Science at the university

A knowledge graph on queer history

Population Assignment using Genetic, Non-genetic or Integrated Data in a Machine-learning Framework. Methods in Ecology and Evolution. 2018;9:439–446.

Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.

Baltica: integrated differential junction usage

KiMONo is a network inference tool for multi-omics datasets. The multi-omics network is calculated by sparse-group-LASSO regression and can incorporate prior biological information using protein-protein Interactions.

Collection of scripts for gene age sorting and multi-omics data mining and analysis

CHIP-seq and RNA-seq integration tutorial

Integrating pathways and related knowledge in a multilayer framework

TDI Capstone Project

A statistical approach for meta-analyzing adjusted and unadjusted estimates from epidemiological cohorts/studies.

Batch-Effect Reduction Trees

multimedia is an R package for multimodal mediation analysis of microbiome data. It has been designed to help integration of relative abundance, survey, and metabolomic data through causal mediation analysis.

R package for integrative analysis of several related data matrices

A multi-level integration algorithm for sensitive integration, reference-mapping, and cell state identification in single-cell data.