MDSINE2 Dataset Inference Analysis

MDSINE2 Inference Analysis files. This archive contains the output from the inference stage of the dataset (MCMC samples) using ten different seeds. Each ZIP archive has been split due to technical limitations while uploading large files through Zenodo's web API.

For the full project/source pipeline, refer to https://github.com/gerberlab/MDSINE2_Paper.

1) To download the files, we recommend either our in-house tool (https://github.com/gibsonlab/zenodo_download) or Zenodo's endorsed tool (https://github.com/dvolgyes/zenodo_get).

2) The multi-part ZIP files were created using 7-zip. To unzip it, you should use the "7z x" command. For example, to unpack seed 10 from the command line:

7z x healthy-seed10.zip

3) In the MDSINE2 installation, we provide a command-line interface "mdsine2 extract-posterior" for extracting the MCMC samples from the output of the unpacked ZIP archives (python pickle files). For instance, `mdsine2 extract-posterior -i healthy-seed10/mcmc.pkl -i healthy-seed11/mcmc.pkl ...`

--------

Related zenodo records:

https://doi.org/10.5281/zenodo.16915311 -- MDSINE2 Semisynthetic Dataset

https://doi.org/10.5281/zenodo.16905647 -- MDSINE2 Cross-Validation run (Healthy cohort)

https://doi.org/10.5281/zenodo.16915340 -- MDSINE2 Cross-Validation run (Dysbiotic cohort)