R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

scBubbletree: quantitative tool for visual exploration of scRNA-seq data

Reproduction of SIB course on single cell transcriptomics by mostly using the Seurat pipeline

Instructions, and protocols for ChronoSeq technology

Single cell analysis of Maatz et. al (2025) data

1Cellbio file to Seurat/SingleCellExperiment/Scanpy

Mapping Ambiguity Overdispersion Correction for scRNA-seq

Processing Salmon Alevin bootstrap replicates to account for technical uncertainty before integrating single-cell RNA-seq datasets in Seurat. Note: this project is now available as an R package: https://github.com/sbresnahan/scAmbi

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

scGenePanel is an R package that can be used to create multipanel plots for single cell gene expression metrics

code and data relating to the scLANE revision

This repository is dedicated to curating, organizing, and annotating metadata for scRNA-seq datasets of human breast cancer, with a focus on datasets that include myeloid cells. This work is tied to the Mye-InfoBank project, aiming to enhance data integration, analysis, and reproducibility in breast cancer

Prioritise cell-type-specific gene targets from the Rare Disease Celltyping project.

Repo linked to our recent publication in Science Advances

Taller de la CDSB 2021 sobre análisis de datos de scRNA-seq con Bioconductor

CHARGE Consortium: collaboration for mapping targets from 1000G GWAS on coronary artery calcification (CAC) with Maryam Kavousi, Maxime Bos, Clint L. Miller, and Pat Peyser.

an integrative algorithm to distinguish spatially variable cell subclusters by reconstructing cells onto a pseudo space with spatial transcriptome references

Tutorial for performing scRNA-seq analysis using cellCounts and Seurat

Single cell data analysis tutorials