NicheNet: predict active ligand-target links between interacting cells
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Updated
May 3, 2024 - R
NicheNet: predict active ligand-target links between interacting cells
Fast, sensitive and accurate integration of single-cell data with Harmony
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
R package for High dimensional data analysis and integration with O2PLS!
ADTnorm normalizes the cell surface protein measurement of CITE-seq data, facilitating across batches and across studies data integration.
Saunders, S.P., Farr, M.T., Wright, A.D., Bahlai, C.A., Ribeiro, J.W., Rossman, S., Sussman, A.L., Arnold, T.W., & Zipkin, E.F. 2019. Disentangling data discrepancies and deficiencies with integrated population models. Ecology 100(6): e02714.
FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis
Population Assignment using Genetic, Non-genetic or Integrated Data in a Machine-learning Framework. Methods in Ecology and Evolution. 2018;9:439–446.
Collection of scripts for gene age sorting and multi-omics data mining and analysis
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.
Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.
Baltica: integrated differential junction usage
R package for finding a joint low-rank representation for a collection of matrices with shared row or column entities.
TDI Capstone Project
🌲 Integrating Sample Similarity Information into Latent Class Models: A Tree-Structured Shrinkage Approach
R package for integrative analysis of several related data matrices
CHIP-seq and RNA-seq integration tutorial
Integrating pathways and related knowledge in a multilayer framework
A knowledge graph on queer history
GenePattern module which implements the batch correction algorithm within Seurat.
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