multiome

Multimodal datasets, in MuData format

Chromatin analysis module

Pipeline to process sc-ATAC data with pyCistopic

Analysis code for Amrute, Luo et al., Nature (2024): CITE-seq, single-nucleus multiome and spatial transcriptomics of human heart failure identifying FAP+/POSTN+ fibroblasts and IL-1b-driven immune-fibroblast communication.

Targets-based workflow for processing and analyzing single-nucleus 10x Genomics Multiome data

Code for Walker, Saunders, Rai et al., (2021).

Continuation of a developmental ArchR repo, for chromatin accessibility analysis

Official – El Arkhe

A nextflow workflow that wraps SAMap

snRNA+snATAC multiome of AD DLPFC microglia — chromVAR motif analysis, WNN integration, peak-to-gene linkage, Monocle3 trajectory | Signac · Seurat · R

Multiome (RNA+ATAC from same cell) data generated by Qinyu Zhang in David Bryder's lab. Paper here: https://doi.org/10.7554/eLife.91826.2

Automated sample QC and processing for RNA/ATAC multiome

Accompanying code for analysis of manuscript in Nature Aging: Implications of stress-induced gene expression for hematopoietic stem cell aging studies

Personal bioinformatics cookbook of reusable R, Python and Quarto workflows for single-cell, transcriptomics, multi-omics and biomarker analysis.

SSc skin yields six times fewer fibroblast nuclei than healthy skin in GSE312129, a composition confound for any between-group claim from that dataset.

Reproducible benchmark reranking Signac LinkPeaks candidate peak–gene links from PBMC multiome data, with SCENT validation and explicit promoter-proximity controls.

10x multiome sequencing of 3 independent differentiations of stem-cells to pancreatic islets

WDLized Cell Ranger ARC