Stars
Workshop in omics integration and systems biology
R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
NicheNet: predict active ligand-target links between interacting cells
An extremely long review of R.
📚 Tools and databases for analyzing HLA and VDJ genes.
Methods for detecting doublets in single-cell sequencing data
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
r2mlm: R Package for Calculating R-Squared in Multilevel Models
Rcpp Machine Learning: Fast robust NMF, divisive clustering, and more
R package implementation of Milo for testing for differential abundance in KNN graphs
Coarse-graining of large single-cell RNA-seq data into metacells
Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
Projection example using a human CD8 TIL reference map.
📝 Algorithms and data structures implemented in JavaScript with explanations and links to further readings
All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs
Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.
Methods to compute Local Inverse Simpson's Index (LISI)