polarolouis/human-microbiome-compendium
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  • c59332590d Add seq res 3/3 main Polarolouis 2026-02-24 15:24:14 +01:00
  • b010e17a91 Add seq res 2/3 Polarolouis 2026-02-24 15:23:01 +01:00
  • bd11576f7a Add seq res 1/3 Polarolouis 2026-02-24 15:22:28 +01:00
  • 9cf21b4d07 Add para res 3/3 Polarolouis 2026-02-24 15:21:24 +01:00
  • 8d71e083c1 Add para res 2/3 Polarolouis 2026-02-24 15:19:17 +01:00
  • 2c85bb7e70 Add para res 1/3 Polarolouis 2026-02-24 15:09:59 +01:00
  • e51b568ef5 Add notrans data 3/3 Polarolouis 2026-02-24 15:06:30 +01:00
  • 25345453b5 Add notrans 2/3 Polarolouis 2026-02-24 15:05:01 +01:00
  • e74925a2fb Add part notrans res 1/? Polarolouis 2026-02-24 15:04:13 +01:00
  • a382f61233 Extracting folder Louis 2026-02-24 14:51:46 +01:00
  • 9995e60b20 Begin adding matching graph in multipartite Louis 2026-02-24 14:51:37 +01:00
  • de4984c2c0 Fixing regex Louis 2026-02-24 14:35:46 +01:00
  • 96db7c5169 Code for the multipartite Louis 2026-02-24 14:30:42 +01:00
  • e6c38905b3 Fixing merge lbm seq Louis 2026-02-24 11:30:54 +01:00
  • 88024bd343 The real fix on save_dir creation Louis 2026-02-24 09:43:28 +01:00
  • a8bdeecb3a fix save path Louis 2026-02-23 14:07:18 +01:00
  • 4d5415bbf4 fix Louis 2026-02-23 14:05:52 +01:00
  • d618e1b5d7 Add sge Louis 2026-02-23 14:04:24 +01:00
  • 3a1c84443c BM correct sampling Louis 2026-02-23 14:01:35 +01:00
  • be7453fb9d For merging lbm-seq results Louis 2026-02-23 11:17:58 +01:00
  • e7f41d56f7 Renaming biom data Louis 2026-02-23 11:17:41 +01:00
  • 97b4a43597 Usage of Blockmodels with poisson covariates to correct sequencing effort Louis 2026-02-19 10:40:01 +01:00
  • 6fa32f2157 Multipartite fungus tree with all dist matrix Louis 2026-02-19 10:39:36 +01:00
  • 65e305e297 Update stats panels with sequencing effort Louis 2026-02-19 10:39:15 +01:00
  • 29728d8205 Using GREMLINS from sbm Louis 2026-02-16 15:58:01 +01:00
  • c13fe8bf3e Commentaires sur les différents multipartites Louis 2026-02-16 13:34:43 +01:00
  • e2819c5607 Adding multiple models using dev GREMLINS Louis 2026-02-11 21:41:50 +01:00
  • 09bcd00d6a Adding Fungus Tree data Louis 2026-02-11 17:36:50 +01:00
  • 40068f8d00 Cleaner implementation of benchmark lbm seq Louis 2026-02-10 11:27:05 +01:00
  • 20d26e8634 Working on LBM seq analysis Louis 2026-02-09 17:50:07 +01:00
  • 691ad05b25 Add lbm_seq_data Louis 2026-02-09 17:49:46 +01:00
  • 3477c6e123 Fixing str_split Louis 2026-02-09 15:53:17 +01:00
  • 5f922c1453 Adding ARI and ICL compute Louis 2026-02-09 15:53:01 +01:00
  • 819d4328c0 Modif analysis Louis 2026-02-02 16:34:05 +01:00
  • 1fc536e0f0 Analysing chaillou Louis 2026-02-02 09:33:32 +01:00
  • ec095c69b5 Adding chaillou results Polarolouis 2026-02-02 09:30:01 +01:00
  • 27bfabed06 embedding resources Louis 2026-02-02 09:27:53 +01:00
  • ff0e27eb69 LBMSEQ benchmark : Changing data and save path Louis 2026-02-01 19:28:32 +01:00
  • 40e1b9386c Add script to copy results from tmp dirs Polarolouis 2026-01-30 14:37:50 +01:00
  • d65dc24b3b Add final data Polarolouis 2026-01-30 14:37:02 +01:00
  • dcff0d857b Ignoring tmp Louis 2026-01-30 14:36:25 +01:00
  • 96c5662051 Ignoring tmp in results Louis 2026-01-30 14:35:42 +01:00
  • cb7f459341 Replacing R script by qmd Louis 2026-01-30 14:33:49 +01:00
  • 3a90551f68 Adding more to analysis Louis 2026-01-29 15:06:08 +01:00
  • 7723128f93 Adding new reps Polarolouis 2026-01-29 14:52:09 +01:00
  • 9f589a1fdc Graph for time and size of OTUs Louis 2026-01-29 10:37:32 +01:00
  • 2fc1cf4e65 lbm on phyloseq Louis 2026-01-28 15:55:12 +01:00
  • 05e9bca613 Analysis for increasing size Louis 2026-01-28 15:54:41 +01:00
  • 9abde593fd Stats panel Louis 2026-01-28 15:52:42 +01:00
  • 1fe1656700 Autosave tests Louis 2026-01-28 15:51:17 +01:00
  • d5f1620361 Adding first results for LBM seq Polarolouis 2026-01-28 15:32:58 +01:00
  • 0ce0338111 Adding cores transmission mechanism for the R script Louis 2026-01-27 10:20:19 +01:00
  • 2443c49694 Using long.q and 128 cores Louis 2026-01-27 09:59:10 +01:00
  • 6d6312c5f6 Update SGE script Louis 2026-01-27 09:55:56 +01:00
  • 049e09bb26 Using autosave Louis 2026-01-27 09:54:29 +01:00
  • d46e7e8913 Adding autosave capabilities Louis 2026-01-27 09:52:03 +01:00
  • e236b687ca Adding script to run benchmarks for LBM Seq Louis 2026-01-23 17:03:10 +01:00
  • df319af88d Adding defaults to bm utils Louis 2026-01-23 17:02:27 +01:00
  • e53e3740f6 Fix a typo 'the_data' to 'phylo_data' Louis 2026-01-23 15:30:33 +01:00
  • d7919e3098 Extracting sequential taxo function to utils-bm-seq.R Louis 2026-01-23 15:30:11 +01:00
  • 1df7268419 First draft of working init of LBM sequential Louis 2026-01-23 13:44:59 +01:00
  • 14adda1a36 Working sequential LBM for a given Q Louis 2026-01-19 17:10:59 +01:00
  • 3095f64b99 Adding LBM sequential first draft Louis 2026-01-16 15:41:54 +01:00
  • f5e6e8f05c Added tau propagation Louis 2026-01-16 15:41:16 +01:00
  • 542d9cd271 Add a qmd for stats panel Louis 2026-01-14 16:48:53 +01:00
  • 58b4dce83b utils: add collapse to merge otu by taxonomy Louis 2026-01-14 16:48:43 +01:00
  • 5ef2703efe Adding results for increasing size time for bernoulli emission Polarolouis 2026-01-05 10:18:10 +01:00
  • be8f6d000d Use difftime to stabilize units Louis 2025-12-23 13:15:46 +01:00
  • b2c8ac222b Add analysis for increasing Louis 2025-12-23 13:15:35 +01:00
  • b1fef82630 Adding sbm results for increasing n2 Polarolouis 2025-12-23 13:03:04 +01:00
  • eb1a4e69ac Fix incorrect time and add recursive dir creation Louis 2025-12-22 15:44:23 +01:00
  • 3aac79d151 Creating results dir if doesnt exists Louis 2025-12-22 15:39:01 +01:00
  • 8afd913289 Logs to logs dir Louis 2025-12-22 15:38:48 +01:00
  • cc277dab37 setting correct out list Louis 2025-12-22 15:31:32 +01:00
  • 76e60b3202 Handling 0 case for min and max Louis 2025-12-22 15:29:50 +01:00
  • 3fc242b0b2 Logging to specific files Louis 2025-12-22 15:28:50 +01:00
  • 5c564e4b3b Fix variable attribution Louis 2025-12-22 15:27:14 +01:00
  • 6aed2e2dfe Add sge script Louis 2025-12-22 15:19:18 +01:00
  • 5e8644493e Handling arguments and saving Louis 2025-12-22 15:17:37 +01:00
  • 0d45da0316 Parsing args for max and setting ncores to 64 Louis 2025-12-22 14:40:51 +01:00
  • 32707e2e49 Drafting for computational complexity tests Louis 2025-12-22 14:10:54 +01:00
  • 0f10320fb5 Adding sample biom data Louis 2025-12-22 14:10:28 +01:00
  • bfa58899f9 Adding plots to check Poisson distribution for some sample phyloseq data Louis 2025-12-22 14:10:12 +01:00
  • 18ca3a38eb Adding requirements and draft for using sparseBM package Louis 2025-12-22 14:09:39 +01:00
  • 0c0ed4653c Written on disk otu_matrix.csv.zip Louis 2025-12-22 14:09:14 +01:00
  • 9a26d88ecb Basic stats for OTU and compressing OTU matrix as file Louis 2025-12-22 14:08:45 +01:00
  • eca2c0198c First script for tree sampling Louis 2025-12-22 14:08:07 +01:00
  • 354ee4d528 Load full Louis 2025-11-14 10:52:29 +01:00
  • 3570b94f49 Extracting filewrite and moving libraries Louis 2025-10-17 16:48:23 +02:00
  • 5c955a8478 Beginning multipartite Louis 2025-10-17 16:47:54 +02:00
  • bf571317f4 Create lbm per taxa level Louis 2025-10-17 16:47:41 +02:00
  • 5cf922d69f Perform file existence check in load script Louis 2025-10-13 13:41:05 +02:00
  • ad91ae0ef1 Removed unused variable Louis 2025-10-13 10:29:22 +02:00
  • 47fe4de889 Created a script to generate nice visuals for slides Louis 2025-10-13 10:26:20 +02:00
  • aa97a8f486 Adding utils functions Louis 2025-10-13 10:26:01 +02:00
  • a6298fadcd Using new loading script in easy16s visu Louis 2025-10-13 10:25:50 +02:00
  • 099a654a21 Retrieved European data Louis 2025-10-13 10:25:19 +02:00
  • c952458363 Extracting code to load Europe samples to its own script Louis 2025-10-13 10:25:10 +02:00
  • 8bbfec9e49 Add outfiles directory Louis 2025-09-27 12:03:54 +02:00
  • aa824b130b Added easy16s visualization Louis 2025-08-17 17:25:17 +02:00