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WardDeb merged 1 commit into from
Sep 1, 2026
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docs: public data info, zenodo badge #30

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[![DOI:10.5281/zenodo.21529137](https://img.shields.io/badge/DOI-10.5281/zenodo.21529137-yellow.svg)](https://doi.org/10.5281/zenodo.21529137)

# deeptools 25 repo

## Setup
Expand Down Expand Up @@ -36,3 +38,51 @@ In case you want to run either the benchmark of the example via slurm, an exampl
The results generated from both workflows (benchmark and example workflow), as well as the code to generate figure 1 are included in this repository. To collate/generate the figures in the `figures` directory, simply run:

> pixi run bash figures/collate_figures.sh

## Public data
Both the benchmark as well as the example use publicly available data. The processed version of this data is included in the zenodo archive (and will be downloaded automatically by the respective workflows), the original source data can be retrieved through the accessions listed here.

| Purpose | Modality | Organism | SRA | BioProject | GEO | doi |
| --- | --- | --- | --- | --- | --- | --- |
| benchmark | ChIP - H3K9me3 | Human | SRR28592124 | PRJNA1097546 | GSE263436 | 10.1073/pnas.2412258121 |
| benchmark | RNA | Human | SRR28012902 | PRJNA1078228 | GSE256091 | 10.1158/0008-5472.CAN-23-1551 |
| benchmark | WGS | Human | SRR15494527 | PRJNA752223 | / | / |
| benchmark | ChIP - CENH3 | Wheat | SRR1686799 | PRJNA268976 | GSE63752 | 10.1105/tpc.19.00133 |
| benchmark | RNA | Wheat | SRR27822150 | PRJNA1071712 | GSE254797 | 10.3389/fpls.2024.1401135 |
| benchmark | WGS | Wheat | SRR27887047 | PRJNA956839 | / | 10.1038/s41586-024-07808-z |
| example | NPC_9sca_ctrl_H3K27ac_rep1 | Mouse | SRR15829033 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_H3K27ac_rep2| Mouse | SRR15829034 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_H3K27me3_rep1| Mouse | SRR15829036 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_H3K27me3_rep2| Mouse | SRR15829037 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_H3K4me1_rep1| Mouse | SRR15829042 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_H3K4me1_rep2| Mouse | SRR15829043 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_H3K4me3_rep1| Mouse | SRR15829045 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_H3K4me3_rep2| Mouse | SRR15829046 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_H3K9me3_rep1| Mouse | SRR15829048 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_H3K9me3_rep2| Mouse | SRR15829049 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_input_rep1| Mouse | SRR15829058 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_input_rep2| Mouse | SRR15829059 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_RNA_rep1| Mouse | SRR15829077 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_RNA_rep2| Mouse | SRR15829078 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_ATAC_rep1| Mouse | SRR15829121 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_ATAC_rep2| Mouse | SRR15829122 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_BS_rep1| Mouse | SRR15829019 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ctrl_BS_rep2| Mouse | SRR15829020 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_ATAC_rep1| Mouse | SRR15829084 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_ATAC_rep2| Mouse | SRR15829085 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_BS_rep1| Mouse | SRR15829089 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_BS_rep2| Mouse | SRR15829090 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_H3K27ac_rep1| Mouse | SRR15829101 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_H3K27ac_rep2| Mouse | SRR15829102 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_H3K27me3_rep1| Mouse | SRR15829103 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_H3K27me3_rep2| Mouse | SRR15829104 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_H3K4me1_rep1| Mouse | SRR15829107 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_H3K4me1_rep2| Mouse | SRR15829108 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_H3K4me3_rep1| Mouse | SRR15829109 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_H3K4me3_rep2| Mouse | SRR15829110 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_H3K9me3_rep1| Mouse | SRR15829111 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_H3K9me3_rep2| Mouse | SRR15829124 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_input1_rep1| Mouse | SRR15829131 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_input1_rep2| Mouse | SRR15829132 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_RNA_rep1| Mouse | SRR15829149 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |
| example | NPC_9sca_ko_RNA_rep2| Mouse | SRR15829150 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |