Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).

Normalize CITEseq Data

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

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

Novel joint clustering method with scRNA-seq and CITE-seq data

Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments

scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data

CITE-seq profiling of human PBMCs at baseline and activation conditions

Material for Bioconductor 2023 workshop on interoperation with python

A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.

Project analyzing multi-omics genomics data from a COVID-19 study.

experimental interface between R and scvi-tools

A ShinyApp for visualization and explorering Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) data