Commits · master · Laurent Modolo / yellow_fever · GitLab

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Apr 22, 2021
- update README.md to the last version of the analysis pipeline · 092df231
  Laurent Modolo authored 4 years ago
  
  092df231
- improve img for the clone size · 344acd5f
  Laurent Modolo authored 4 years ago
  
  344acd5f
Dec 04, 2020
- fix fisher alpha slope analysis · 19fd3f3a
  Laurent Modolo authored 4 years ago
  
  19fd3f3a
- fix fisher alpha figure 1 · 967f88e1
  Laurent Modolo authored 4 years ago
  
  967f88e1
Nov 26, 2020
- 0_1_Clone_size.R: add test between earlyer and latest day · 43c3e4ee
  Laurent Modolo authored 4 years ago
  
  43c3e4ee
Nov 19, 2020
- 0_1_Clone_size.R: add annotation · 211a3c56
  Laurent Modolo authored 4 years ago
  
  211a3c56
Nov 12, 2020
- 0_1_Clone_size.R: new bootstrap plots · 3cd500c3
  Laurent Modolo authored 4 years ago
  
  3cd500c3
Nov 05, 2020
- 0_1_Clone_size.R: change points size for clone_diversity plot · 4642bc52
  Laurent Modolo authored 4 years ago
  
  4642bc52
Oct 30, 2020
- 0_1_Clone_size.R: add boostrapp test for clone diversity · f0e1cbc9
  Laurent Modolo authored 4 years ago
  
  f0e1cbc9
Oct 21, 2020
- add src/13_facs_analysis.R · ee2bfcc6
  Laurent Modolo authored 4 years ago
  
  ee2bfcc6
- add 2_6_full_male_donor.R · e700a107
  Laurent Modolo authored 4 years ago
  
  e700a107
- clonality_paper: analyse shuffling clone experiment · 0818134e
  Laurent Modolo authored 4 years ago
  
  0818134e
Oct 16, 2020
- fix clonality shuffling DEA · 83661882
  Laurent Modolo authored 4 years ago
  
  83661882
- 00_function.R: add janitor to packages list · 6ce6b601
  Laurent Modolo authored 4 years ago
  
  6ce6b601
Oct 15, 2020
- fix sge scripts for clonality analysis · 6323bf70
  Laurent Modolo authored 4 years ago
  
  6323bf70
- 00_function.R: rm DAHRMA from packages list · bbb3beb1
  Laurent Modolo authored 4 years ago
  
  bbb3beb1
- clonality_paper: split sge script between size 10 and 3 · d51b8134
  Laurent Modolo authored 4 years ago
  
  d51b8134
- clonality_paper_shuffling_clone.sge change R version to 4.0.3 · bda1b94f
  Laurent Modolo authored 4 years ago
  
  bda1b94f
- clonality_paper_shuffling_clone.sge: rename job · a76b3095
  Laurent Modolo authored 4 years ago
  
  a76b3095
- clonality_paper_shuffling_clone.sge: fix queue option · d445f56e
  Laurent Modolo authored 4 years ago
  
  d445f56e
- clonality_paper: add sge scripts · 31584c78
  Laurent Modolo authored 4 years ago
  
  31584c78
- clonality_paper.R: add shuffling step to test clonality DEA · d71240f9
  Laurent Modolo authored 4 years ago
  
  d71240f9
Oct 13, 2020
- clonality_paper.R: test of logit DEA · fba99734
  Laurent Modolo authored 4 years ago
  
  fba99734
Oct 09, 2020
- clonality_paper.R: test on heatmap · 24dd253f
  Laurent Modolo authored 4 years ago
  
  24dd253f
Oct 08, 2020
- clonality_paper.R: test on heatmap · fde1f52a
  Laurent Modolo authored 4 years ago
  
  fde1f52a
- fix DEA for variable with 1 in the name · 17425f65
  Laurent Modolo authored 4 years ago
  
  17425f65
- clonality_paper.R: DEA analysis accounting for PCA 1 and 2 for PLS genes · ef2e932d
  Laurent Modolo authored 4 years ago
  
  ef2e932d
Oct 02, 2020
- clonality_paper.R: analysis of clonal data (PLS and DEA) · 0dfc8420
  Laurent Modolo authored 4 years ago
  
  0dfc8420
- 00_function.R: improve PLS sce handling · 9c6f1c82
  Laurent Modolo authored 4 years ago
  
  9c6f1c82
Jul 10, 2020
- src/00_DEA.R: add script to run DEA · dd5491e8
  Laurent Modolo authored 4 years ago
  
  dd5491e8
Jun 12, 2020
- 05_large_clones.R: add example of clonality analysis · 184f063a
  Laurent Modolo authored 4 years ago
  
  184f063a
Jun 10, 2020
- 00_function.R: upgrade DEA function to handle LRT of mixed effects · 20a2d5a8
  Laurent Modolo authored 4 years ago
  
  20a2d5a8
- 04_cell_type_DEA_PLS.R: add heatmap plot and fix pval correction · 10eb7e15
  Laurent Modolo authored 4 years ago
  
  10eb7e15
- 01_QC.R: add code to export file name list to Joana · 317ec599
  Laurent Modolo authored 4 years ago
  
  317ec599
- 00_function.R: add somme function documentation · 05bcdf3d
  Laurent Modolo authored 4 years ago
  
  05bcdf3d
May 16, 2020
- src/00_functions.R: fix DEA genes order · a5846974
  Laurent Modolo authored 4 years ago
  
  a5846974
May 15, 2020
- 04_cell_type_DEA_PLS.R: add output resulsts as csv · 4ee5cd40
  Laurent Modolo authored 4 years ago
  
  4ee5cd40
- src/00_functions.R: add comment to install packages · d18e0d7c
  Laurent Modolo authored 4 years ago
  
  d18e0d7c
- 04_cell_type_DEA_PLS.R: add diagnostic plots · 07b830ca
  Laurent Modolo authored 4 years ago
  
  07b830ca
- 00_function.R: add cell_type color palette · b1b9de59
  Laurent Modolo authored 4 years ago
  
  b1b9de59