Commits · master · SPSP / sarscov2 / cluster-detection

Browse files

May 22, 2023
- Upload virus_in_paper.zip · 03c21185
  bcabrera authored May 22, 2023
  
  03c21185
- Remove old SPSP dump · 288dc65e
  bcabrera authored May 22, 2023
  
  288dc65e
May 01, 2023
- Add viruses used in paper · 25d6cf5d
  bcabrera authored May 1, 2023
  
  25d6cf5d
Apr 21, 2023
- Removed global paths. · 9b05e3bf
  bcabrera authored Apr 21, 2023
  
  9b05e3bf
- Update analysis of 0-snp time windows · fc6dc10c
  bcabrera authored Apr 21, 2023
  
  fc6dc10c
- Remove draft paper notebook · 882cb265
  bcabrera authored Apr 21, 2023
  
  882cb265
Apr 20, 2023
- Clean paper notebook · dc7b9d51
  bcabrera authored Apr 20, 2023
  
  dc7b9d51
Feb 10, 2023
- Updated normalized correlation plot, computed boxplots for superspreder... · a5576fd1
  bcabrera authored Feb 10, 2023
  a5576fd1
Feb 03, 2023
- Investigate filtered sequences omicron · 38bdff81
  bcabrera authored Feb 3, 2023
  
  38bdff81
Feb 02, 2023
- Add cluster density normalized by the number of sequences in the cluster analysis · d4f4a224
  bcabrera authored Feb 2, 2023
  
  d4f4a224
Nov 04, 2022
- Execute latest results · 4d969fc3
  bcabrera authored Nov 4, 2022
  
  4d969fc3
- Update License · fcb0c3e4
  bcabrera authored Nov 4, 2022
  
  fcb0c3e4
- Beautify readme.md · 971a770b
  bcabrera authored Nov 4, 2022
  
  971a770b
- Add readme pics · e2c5f943
  bcabrera authored Nov 4, 2022
  
  e2c5f943
- Use get_snp_cluster package & document · 2d57b225
  bcabrera authored Nov 4, 2022
  
  2d57b225
- Repository restructure · a84d3551
  bcabrera authored Nov 4, 2022
  
  a84d3551
- Update README.md · 8b476f79
  bcabrera authored Nov 4, 2022
  
  8b476f79
- Update README.md · f9a94010
  bcabrera authored Nov 4, 2022
  
  f9a94010
Oct 27, 2022
- Clean SPSP-paper-plots.ipynb · 8ebd662e
  bcabrera authored Oct 27, 2022
  
  8ebd662e
Oct 25, 2022
- Add paper plots notebook · 317c0c67
  bcabrera authored Oct 25, 2022
  
  317c0c67
- make cluster tool callable · c0f64724
  bcabrera authored Oct 25, 2022
  
  c0f64724
May 26, 2022
- Merge branch 'master' of https://gitlab.sib.swiss/SPSP/sarscov2/cluster-detection · 8195ec2d
  bcabrera authored May 26, 2022
  
  8195ec2d
- Replace hierarchical clustering by UnionFind to merge 1-SNP clusters · c7d39f0f
  bcabrera authored May 26, 2022
  
  c7d39f0f
May 19, 2022
- Upload New File · 366ba1fb
  bcabrera authored May 19, 2022
  
  366ba1fb
- Delete SPSP-dump_220421.tsv.zip · 4e7c651f
  bcabrera authored May 19, 2022
  
  4e7c651f
- Bash script · d1e6b442
  bcabrera authored May 19, 2022
  
  d1e6b442
- Merge branch 'master' of https://gitlab.sib.swiss/SPSP/sarscov2/cluster-detection · 2b88164c
  bcabrera authored May 19, 2022
  
  2b88164c
- Code update for new spsp data format · 1a7287a0
  bcabrera authored May 19, 2022
  
  1a7287a0
May 09, 2022
- Dump1-non-sensitive · de7e5740
  aneves authored May 9, 2022
  
  de7e5740
- Add new directory · 7c0a5868
  aneves authored May 9, 2022
  
  7c0a5868
Dec 09, 2021
- Update README.md to add license · 9286d44f
  aneves authored Dec 9, 2021
  
  9286d44f
Nov 19, 2021
- Update snakemake-minimal version. · e4acbc8c
  bcabrera authored Nov 19, 2021
  
  e4acbc8c
- Document and clean code. · 4b872681
  bcabrera authored Nov 19, 2021
  
  4b872681
- Remove HC_THRESHOLD input parameter. · 174e85a7
  bcabrera authored Nov 19, 2021
  
  174e85a7
Oct 25, 2021
- Fix output in clusters summary · 1acd51dc
  bcabrera authored Oct 25, 2021
  
  1acd51dc
- Small updates to cluster merge. · 3b8561d5
  bcabrera authored Oct 25, 2021
  
  3b8561d5
Oct 22, 2021
- Fix libraries and dependency bugs · 3cd1ccd3
  bcabrera authored Oct 22, 2021
  
  3cd1ccd3
- Use hierarchical clustering as method to merge 1-SNP clusters · 6b121e86
  bcabrera authored Oct 22, 2021
  
  6b121e86
Oct 15, 2021
- Remove personal directories. · 0385fa2e
  bcabrera authored Oct 15, 2021
  
  0385fa2e
- Update README · 9ce02353
  bcabrera authored Oct 15, 2021
  
  9ce02353