MUFFIN : A suite of tools for the analysis of functional sequencing data - Example input data

This repository contains the data required to run the example notebooks and to reproduce the figures from the paper : 

MUFFIN : A suite of tools for the analysis of functional sequencing data

Pierre de Langen, Benoit Ballester

bioRxiv 2023.12.11.570597; doi: https://doi.org/10.1101/2023.12.11.570597

Source code is located here :

https://github.com/pdelangen/Muffin

10k_pbmc_gene/ contains the data for 10k pbmc dataset in standard 10x sparse count table format.

genome_annot/ contains gencode v38 and chromosomes for the human (used for gene set enrichment analyses)

GO_files/ contains gene set information retrieved from the g:ProfileR website.

immune_chip/ contains the data required to re-run the ChIP-seq analyses, it will require to also launch the dl_data.smk to retrieve the data from ENCODE.

tcga_atac/ contains the sample-genomic region ATAC tag count table, as well as the sample metadata and a gene set file of cancer hallmark genes.

scATAC/  contains the cell barcode-genomic region ATAC tag count table, as well as the barcode metadata and the 10k pbmc dataset pre-analyzed in h5 AnnData format.