Datasets and supplemental information accompanying scANANSE
Creators
- 1. Radboud University
Description
This repository contains supplementary files from the paper: "scANANSE: gene regulatory network and motif analysis of single-cell clusters" as well as several accompanying datasets.
The supplementary files:
- Install_Rstudio.pdf
- AnanseScanpy_equivalent.pdf
The pre-processed Seurat object and the two pre-processed Scanpy objects can be used to run the scANANSE pipeline with:
- preprocessed_PBMC.Rds
- rna_PBMC.h5ad
- atac_PBMC.h5ad
Additional raw data, used to construct the pre-processed objects, supplemented from:
https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/pbmc_granulocyte_sorted_10k_filtered_feature_bc_matrix.h5, https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz, https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz.tbi,
https://atlas.fredhutch.org/data/nygc/multimodal/pbmc_multimodal.h5seura
Files
AnanseScanpy_equivalent.pdf
Files
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Additional details
Related works
- Is supplemented by
- Journal article: 10.12688/f1000research.130530.1 (DOI)