Commits · master · BDS / GeneDER / GeneDER_core

23 Dec, 2022 1 commit
- Merge branch 'develop' into 'master' · e2890318
  Leon-Charles Tranchevent authored Dec 23, 2022
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Final MR before leaving.

See merge request !6
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  e2890318
20 Dec, 2022 1 commit
- Added a script to plot gene expression profiles for a different differential... · 85591a2f
  Leon-Charles Tranchevent authored Dec 20, 2022
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Added a script to plot gene expression profiles for a different differential analysis (PD vs control).
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  85591a2f
12 Oct, 2022 1 commit
- Added the version numbers to the list of packages. · 0a368848
  Leon-Charles Tranchevent authored Oct 12, 2022
  
  0a368848
10 Oct, 2022 2 commits
- Cleaning data repositories in step 08. · c9250307
  Leon-Charles Tranchevent authored Oct 10, 2022
  
  c9250307
- Merge branch 'develop' into 'master' · 89c5d2db
  Leon-Charles Tranchevent authored Oct 10, 2022
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Refactoring of the differential expression analysis as to include more...

See merge request !5
```
  89c5d2db
07 Oct, 2022 1 commit
- Corrected configuration for the global case/control analysis (PMBT) · bfa481e8
  Leon-Charles Tranchevent authored Oct 07, 2022
  
  bfa481e8
05 Oct, 2022 1 commit
- Refactoring step 05-Get_DEGs · 69aabf24
  Leon-Charles Tranchevent authored Oct 05, 2022
  
  69aabf24
23 Sep, 2022 1 commit
- Code refactoring / style harmonizing. · b1db09d0
  Leon-Charles Tranchevent authored Sep 23, 2022
  
  b1db09d0
22 Sep, 2022 1 commit
- Simplified step 08 (regulatory network analysis) to remove all unnecessary / obsolete scripts. · 65d3a255
  Leon-Charles Tranchevent authored Sep 22, 2022
  
  65d3a255
21 Sep, 2022 3 commits
- Harmonizing the README files. · 3498eba2
  Leon-Charles Tranchevent authored Sep 21, 2022
  
  3498eba2
- Removing unnecessary files and cleaning the launchers / Makefiles. · 0c50a6da
  Leon-Charles Tranchevent authored Sep 21, 2022
  
  0c50a6da
- Default configuration for the main meta-analysis. · 9f0e36c1
  Leon-Charles Tranchevent authored Sep 21, 2022
  
  9f0e36c1
07 Sep, 2022 2 commits
- Adapted the functional enrichment and regulatory analysis to the new file formats. · dc4f958f
  Leon-Charles Tranchevent authored Sep 07, 2022
  
  dc4f958f
- Added the Beta values / standard errors to the output of the meta-analysis. · e57831cc
  Leon-Charles Tranchevent authored Sep 07, 2022
  
  e57831cc
05 Sep, 2022 1 commit
- Refactored the integration step to accomodate the latest changes (e.g., PMI/RIN). · 5059ab2f
  Leon-Charles Tranchevent authored Sep 05, 2022
  
  5059ab2f
25 Aug, 2022 1 commit
- Computation of the weighted SD added to the meta-analysis (in addition to the weighted mean). · a7a0e772
  Leon-Charles Tranchevent authored Aug 25, 2022
  
  a7a0e772
24 Aug, 2022 3 commits
- Updated the RIM correlations model generation. · c8444f94
  Leon-Charles Tranchevent authored Aug 24, 2022
  
  c8444f94
- Included RIM correlation models (as an alternative to include RIM as a covariate). · 4ff9170c
  Leon-Charles Tranchevent authored Aug 24, 2022
  
  4ff9170c
- Refactoring the covariate correlation analysis (more complete analysis). · 16ca2fd9
  Leon-Charles Tranchevent authored Aug 24, 2022
  
  16ca2fd9
11 Aug, 2022 2 commits
- Refactoring of the differential expression analysis as to include more... · 33371747
  Leon-Charles Tranchevent authored Aug 11, 2022
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Refactoring of the differential expression analysis as to include more covariates (incl. PMI / RIN).
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  33371747
- Better handling of the log files for scripts that are run for all datasets in any case. · 2c6ffdc4
  Leon-Charles Tranchevent authored Aug 11, 2022
  
  2c6ffdc4
10 Aug, 2022 6 commits
- Added covariate analysis (PVCA and correlation based analysis). · a0d45a19
  Leon-Charles Tranchevent authored Aug 10, 2022
  
  a0d45a19
- Moved some R functions to the local library file. · bf516694
  Leon-Charles Tranchevent authored Aug 10, 2022
  
  bf516694
- New dataset / project configuration (with PVCA related descriptors). · 82670b2a
  Leon-Charles Tranchevent authored Aug 10, 2022
  
  82670b2a
- New configuration for the scRNA-seq data analyses. · caf56ed9
  Leon-Charles Tranchevent authored Aug 10, 2022
  
  caf56ed9
- Adapted launchers to new HPC configuration (wrt updated software set) 1/2. · 64951090
  Leon-Charles Tranchevent authored Aug 10, 2022
  
  64951090
- Updated the license and simplified the Makefile. · e13ef7ee
  Leon-Charles Tranchevent authored Aug 10, 2022
  
  e13ef7ee
24 May, 2022 3 commits
- New enrichment procedure using the new FDR corrected values. · 57be1257
  Leon-Charles Tranchevent authored May 24, 2022
  
  57be1257
- Added the detection of the sex-neutral genes. · 86e2d217
  Leon-Charles Tranchevent authored May 24, 2022
  
  86e2d217
- Modified MODULEPATH for iris computation. · f1774dd7
  Leon-Charles Tranchevent authored May 24, 2022
  
  f1774dd7
05 Apr, 2022 4 commits
- Merge branch 'develop' into 'master' · cc405abb
  Leon-Charles Tranchevent authored Apr 05, 2022
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Merge branch 'develop' into 'master'

See merge request !4
```
  cc405abb
- Refined regulatory network scripts: new GeneGo release, replaced Dorothea by Funki-Dorothea. · 1bbcf0a0
  Leon-Charles Tranchevent authored Apr 05, 2022
  
  1bbcf0a0
- Refined functional enrichment method (no more GSEA, no DO). · e19d2295
  Leon-Charles Tranchevent authored Apr 05, 2022
  
  e19d2295
- New method for sex-specific / sex-dimorphic gene identification, plus new FDR... · 3f2bea40
  Leon-Charles Tranchevent authored Apr 05, 2022
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New method for sex-specific / sex-dimorphic gene identification, plus new FDR correction (sexes combined).
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  3f2bea40
18 Feb, 2022 1 commit
- Updated workflow for the latest toolset on iris and corrected a small issue... · 43c4ad10
  Leon-Charles Tranchevent authored Feb 18, 2022
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Updated workflow for the latest toolset on iris and corrected a small issue with the gender-dimorphic genes.
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  43c4ad10
25 Nov, 2021 1 commit

Merge branch 'develop' into 'master' · 4aa9bf44

Leon-Charles Tranchevent authored Nov 25, 2021

Updated license and documentation for PPC - cleaning of some unnecessary files

See merge request !3

4aa9bf44

23 Nov, 2021 4 commits
- Updated the list of required R packages to include the scRNA packages. · d4e5a666
  Leon-Charles Tranchevent authored Nov 23, 2021
  
  d4e5a666
- Cleaning of step 09 to remove unnecessary files. · cdbfd9da
  Leon-Charles Tranchevent authored Nov 23, 2021
  
  cdbfd9da
- Updated main documentation to include more detailed instructions for all steps of the workflow. · 2b27e4ad
  Leon-Charles Tranchevent authored Nov 23, 2021
  
  2b27e4ad
- Updated individual README files. · 1fb1065b
  Leon-Charles Tranchevent authored Nov 23, 2021
  
  1fb1065b