Data availability for GigaScience submission

[dhimmel]

We've submitted this manuscript to GigaScience (GIGA-D-23-00002). Part of the submission process is an editorial check to ensure data availability. Super excited to see a journal taking such proactive measures.

The check identified some data that we need to better document, export, and upload to GigaDB. Quoting from an email from Yannan Fan on 2023-01-11:

Dear Casey S. Greene,

At GigaScience Press we have strict transparency and reproducibility policies; to ensure this is maintained it is imperative that all data and tools required to reproduce your manuscript are available to the reviewers and ultimately the readers. To facilitate this we have developed GigaDB, which is the repository used to host data and tools associated with articles in GigaScience and GigaByte. You can see a complete workflow of the combined submission process here. This email represents the step labeled as "provide authors with private FTP login".

I have had a quick read through your manuscript. To enable full reproducibility and transparency please follow these instructions on how to make your data available:

• Please read the guidelines for submission of software data: http://gigadb.org/site/guidesoftware

• You should include a list of md5sum values for all files uploaded so that we can confirm file integrity after transfer.

• Please also include a readme.txt file listing all files with a 1 line description of each.

  • Please provide the raw data underlying Figure 4A-B, Figure 5, Figure 6A-C, Figure 7, and Figure 9.

I've opened this issue so we can coordinate and track progress fulfilling this data request.

[dhimmel]

All figures based on data are generated by the https://github.com/greenelab/xswap-analysis repository. They are embedded in the manuscript directly from their source URLs:

Expand for figure source links

## Figure 1 https://github.com/greenelab/xswap-manuscript/blob/523d4aa41ea10f2705b5df564604ba96bae7dde6/content/02.body.md#L19 ## Figure 3 https://github.com/greenelab/xswap-manuscript/blob/523d4aa41ea10f2705b5df564604ba96bae7dde6/content/02.body.md?plain=1#L119 ## Figure 6 https://github.com/greenelab/xswap-manuscript/blob/523d4aa41ea10f2705b5df564604ba96bae7dde6/content/02.body.md?plain=1#L229 ## Figure 7 https://github.com/greenelab/xswap-manuscript/blob/523d4aa41ea10f2705b5df564604ba96bae7dde6/content/02.body.md?plain=1#L271 ## Figure 8 https://github.com/greenelab/xswap-manuscript/blob/523d4aa41ea10f2705b5df564604ba96bae7dde6/content/02.body.md?plain=1#L285 ## Figure 9 https://github.com/greenelab/xswap-manuscript/blob/523d4aa41ea10f2705b5df564604ba96bae7dde6/content/90.back-matter.md?plain=1#L38

[dhimmel]

Updates on this issue:

• @zietzm regenerated a large number of data files that were lost during the Greene Lab move in https://github.com/greenelab/xswap-analysis/pull/26.
• Some datasets with randomness involved changed slightly leading to some figures changing slightly, but with no change in interpretation. Updates to manuscript in https://github.com/greenelab/xswap-manuscript/pull/66
• @zietzm materialized data for the figures, available in the data/figure directory
• We deposited the xswap analysis repo to Zenodo in https://github.com/greenelab/xswap-analysis/issues/27 and https://github.com/greenelab/xswap-manuscript/commit/56c13999c4d1184a247dec65bdae5a906e08f5d3

[dhimmel]

Noting that the GigaDB entry is now online at https://doi.org/10.5524/102479, which takes snapshots of project repositories.