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Polarolouis d5f1620361 Adding first results for LBM seq
2026-01-28 15:32:58 +01:00
data Adding sample biom data 2025-12-22 14:10:28 +01:00
results Adding first results for LBM seq 2026-01-28 15:32:58 +01:00
sge_scripts Adding cores transmission mechanism for the R script 2026-01-27 10:20:19 +01:00
.gitignore Add outfiles directory 2025-09-27 12:03:54 +02:00
.gitlab-ci.yml CI work 2025-05-16 10:56:53 +02:00
benchmark_lbm_seq.R Adding cores transmission mechanism for the R script 2026-01-27 10:20:19 +01:00
colSBM-on-HMC.R sqdf 2025-05-19 12:17:52 +02:00
easy16s-visu.R Using new loading script in easy16s visu 2025-10-13 10:25:50 +02:00
generate-figures.R Created a script to generate nice visuals for slides 2025-10-13 10:26:20 +02:00
increasing_size_analysis.R Add analysis for increasing 2025-12-23 13:15:35 +01:00
increasing_size_test.R Use difftime to stabilize units 2025-12-23 13:15:46 +01:00
lbm-per-taxa.R Create lbm per taxa level 2025-10-17 16:47:41 +02:00
lbm_at_diff_taxo_seq.R Extracting sequential taxo function to utils-bm-seq.R 2026-01-23 15:30:11 +01:00
lbm_full_mat.R Basic stats for OTU and compressing OTU matrix as file 2025-12-22 14:08:45 +01:00
lbm_phyloseq_test.R Adding plots to check Poisson distribution for some sample phyloseq data 2025-12-22 14:10:12 +01:00
load-europe.R Load full 2025-11-14 10:52:29 +01:00
load-full.R Load full 2025-11-14 10:52:29 +01:00
multipartite-lbm.R Beginning multipartite 2025-10-17 16:47:54 +02:00
progressive-tree-sampling.R First script for tree sampling 2025-12-22 14:08:07 +01:00
README.md [ci skip] Rendered README.md after changes 2025-05-16 09:09:05 +00:00
README.qmd Fixing wrong title 2025-05-16 11:08:30 +02:00
references-local.bib Init repo 2025-05-15 17:30:27 +02:00
requirements.txt Adding requirements and draft for using sparseBM package 2025-12-22 14:09:39 +01:00
retrieve-data.R Updating data to 1.1.0 and adding full list of matrices and full supinfo 2025-05-19 11:21:26 +02:00
sparselbm_full_mat.py Adding requirements and draft for using sparseBM package 2025-12-22 14:09:39 +01:00
stats_panel.qmd Add a qmd for stats panel 2026-01-14 16:48:53 +01:00
utils-bm-seq.R Adding autosave capabilities 2026-01-27 09:52:03 +01:00
utils.R Fix a typo 'the_data' to 'phylo_data' 2026-01-23 15:30:33 +01:00

README.md

Human Microbiome Compendium

This repository will host the code for my PhD work on data from the Human Microbiome Compendium detailled in Abdill et al. (2025).

The folder data contain the networks as edgelists and the projects metadata.

Abdill, Richard J., Samantha P. Graham, Vincent Rubinetti, Mansooreh Ahmadian, Parker Hicks, Ashwin Chetty, Daniel McDonald, et al. 2025. “Integration of 168,000 Samples Reveals Global Patterns of the Human Gut Microbiome.” Cell 188 (4): 1100–1118.e17. https://doi.org/10.1016/j.cell.2024.12.017.