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Louis 96c5662051 Ignoring tmp in results
2026-01-30 14:35:42 +01:00
data Adding sample biom data 2025-12-22 14:10:28 +01:00
results Adding new reps 2026-01-29 14:52:34 +01:00
sge_scripts Adding cores transmission mechanism for the R script 2026-01-27 10:20:19 +01:00
.gitignore Ignoring tmp in results 2026-01-30 14:35:42 +01:00
.gitlab-ci.yml CI work 2025-05-16 10:56:53 +02:00
analysis_benchmark_lbm_seq.qmd Replacing R script by qmd 2026-01-30 14:33:49 +01:00
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 Analysis for increasing size 2026-01-28 15:55:17 +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 Autosave tests 2026-01-28 15:55:17 +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 lbm on phyloseq 2026-01-28 15:55:17 +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 Stats panel 2026-01-28 15:55:17 +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.