Commits · main · GoodmanLab / Cat Food - Reboul et al. 2025 · GitLab

Sep 30, 2025
- Upload description file of supplementary data files · 38cf4f4c
  Guillaume Reboul authored Sep 30, 2025
  
  38cf4f4c
- Upload Supplementary Data 5 · 545a20cc
  Guillaume Reboul authored Sep 30, 2025
  
  545a20cc
- Upload Supplementary Data 4 · 2282aceb
  Guillaume Reboul authored Sep 30, 2025
  
  2282aceb
- Upload Supplementary Data 3 · a885230e
  Guillaume Reboul authored Sep 30, 2025
  
  a885230e
- Upload Supplementary Data 2 · b0fd617a
  Guillaume Reboul authored Sep 30, 2025
  
  b0fd617a
- Upload Supplementary Data 1 · 720d78df
  Guillaume Reboul authored Sep 30, 2025
  
  720d78df
- Edit README.md following acceptance and release of article · 384f10e2
  Guillaume Reboul authored Sep 30, 2025
  
  384f10e2
Aug 22, 2025
- Edit doCommands_AMRpanel.sh with correct python scripts names · f43f835e
  Guillaume Reboul authored Aug 22, 2025
  
  f43f835e
- Upload missing file with annotations of panel AMR genes · d589b519
  Guillaume Reboul authored Aug 22, 2025
  
  d589b519
Jul 31, 2025
- Edit README.md with clarification of doCommands files and update on manuscript status · aad121b7
  Guillaume Reboul authored Jul 31, 2025
  
  aad121b7
- Adding here a directory to contain excel files provided as Supplementary Data with the manuscript · a1086ea7
  Guillaume Reboul authored Jul 31, 2025
  
  a1086ea7
Apr 28, 2025
- Upload New File with AMRpanel data needed as input for script AMRpanel.R and... · 86387600
  Guillaume Reboul authored Apr 28, 2025
  86387600
Apr 21, 2025
- Add new file containing command lines used to produce Qiime results for 16S rRNA gene amplicons · 4f3893ae
  Guillaume Reboul authored Apr 21, 2025
  
  4f3893ae
Aug 09, 2024
- Update README.md · c5aebe8e
  Guillaume Reboul authored Aug 09, 2024
  c5aebe8e
Aug 08, 2024
- command line files to replicate analyses yielding the datasets used in R for figure and ms · 093a98ac
  Guillaume Reboul authored Aug 08, 2024
  
  093a98ac
- Update AMR_isolates.R · 70ac4438
  Guillaume Reboul authored Aug 08, 2024
  70ac4438
- Update AMR_panel.R · 73a4d898
  Guillaume Reboul authored Aug 08, 2024
  73a4d898
- Update isolate_presence_vs_metadata.R · f19631cc
  Guillaume Reboul authored Aug 08, 2024
  
  f19631cc
- Update AMR_panel.R · 6df8c8af
  Guillaume Reboul authored Aug 08, 2024
  
  6df8c8af
- Update AMR_isolates.R · c1faad47
  Guillaume Reboul authored Aug 08, 2024
  
  c1faad47
- Delete TableS1_Samples_metadata.tsv.txt because at main folder now · 3bd1bd33
  Guillaume Reboul authored Aug 08, 2024
  
  3bd1bd33
- Metadata tsv file derived from Excel Table S1 in manuscript · d6d7ff24
  Guillaume Reboul authored Aug 08, 2024
  
  d6d7ff24
- contains all the coverage files, need to unzip to run python scripts · 0e8c3886
  Guillaume Reboul authored Aug 08, 2024
  
  0e8c3886
- directory with all the Raw coverage files from Illumina Amplicon tool ran on Basespace · c3a55a58
  Guillaume Reboul authored Aug 08, 2024
  
  c3a55a58
- python script to add annotation to the file containing the merged coverage files · ab7f29e1
  Guillaume Reboul authored Aug 08, 2024
  
  ab7f29e1
- python script to merge all coverage files together · e8bfa5be
  Guillaume Reboul authored Aug 08, 2024
  
  e8bfa5be
- folder to contain all files needed to run those analyses · 3e9d15e6
  Guillaume Reboul authored Aug 08, 2024
  
  3e9d15e6
- Update AMR_isolates.R · d09af910
  Guillaume Reboul authored Aug 08, 2024
  d09af910
- Samples metadata exported from Excel table S1 · 6752a6dd
  Guillaume Reboul authored Aug 08, 2024
  
  6752a6dd
- AMRfinderPlus raw outputs compiled for all of our sequenced isolates · 473ce7c1
  Guillaume Reboul authored Aug 08, 2024
  
  473ce7c1
- Compiled raw output from Deepasmid on our isolates · b5225157
  Guillaume Reboul authored Aug 08, 2024
  
  b5225157
- Upload New File · d565de9b
  Guillaume Reboul authored Aug 08, 2024
  
  d565de9b
- Update AMR_isolates.R · 1e5264e3
  Guillaume Reboul authored Aug 08, 2024
  1e5264e3
Aug 07, 2024
- directory will contain output files from bioinformatics analyses on Isolates used in R later · b9dddd5d
  Guillaume Reboul authored Aug 07, 2024
  
  b9dddd5d
Aug 06, 2024
- Update CSS1.R · 8e904356
  Guillaume Reboul authored Aug 06, 2024
  8e904356
- Excel file of manually curated CSS1 taxonomy for R analyses (then exported in tsv) · 87c42c0c
  Guillaume Reboul authored Aug 06, 2024
  
  87c42c0c
- manually curated CSS1 taxonomy for R analyses · e04cb655
  Guillaume Reboul authored Aug 06, 2024
  
  e04cb655
- R script to plot Figures S6 and S4 using Clostridium Stricto Sensus manually... · 6a3f3dcf
  Guillaume Reboul authored Aug 06, 2024
  6a3f3dcf
- ASV table produced by Qiime pipeline · 9eb44608
  Guillaume Reboul authored Aug 06, 2024
  
  9eb44608
- taxonomy of ASV produced by Qiime pipeline · 1dd48b4d
  Guillaume Reboul authored Aug 06, 2024
  
  1dd48b4d