Commits · 63b80f956fe3883216a0e9238f90b702fc72aaab · BDS / GeneDER / GeneDER_core · GitLab

27 Mar, 2020 1 commit
- Revision of the limma strategy with respect to the potential experimental batches. · 63b80f95
  Leon-Charles Tranchevent authored Mar 27, 2020
  
  63b80f95
23 Mar, 2020 1 commit
- CARNIVAL regulatory networks: fine-tunning and parameter exploration. · d9be7f6f
  Leon-Charles Tranchevent authored Mar 23, 2020
  
  d9be7f6f
16 Mar, 2020 1 commit
- Scripts to use CARNIVAL for regulatory network extraction (second step). · bc6b5621
  Leon-Charles Tranchevent authored Mar 16, 2020
  
  bc6b5621
13 Mar, 2020 1 commit
- Scripts to use CARNIVAL for regulatory network extraction (first step). · 75649021
  Leon-Charles Tranchevent authored Mar 13, 2020
  
  75649021
05 Mar, 2020 1 commit
- Added the GRN creation for the MA+RS analysis · 7d2b53e4
  Leon-Charles Tranchevent authored Mar 05, 2020
  
  7d2b53e4
04 Mar, 2020 3 commits
- Added the enrichment analysis for the MA+RS integration. · a661ba2b
  Leon-Charles Tranchevent authored Mar 04, 2020
  
  a661ba2b
- Updated the documentation (README.md files). · dd6b7c73
  Leon-Charles Tranchevent authored Mar 04, 2020
  
  dd6b7c73
- Added a script to compare the latest integration (MA+RS) to the earliest one (MA only). · f824778b
  Leon-Charles Tranchevent authored Mar 04, 2020
  
  f824778b
21 Feb, 2020 1 commit
- RNA-seq data integration (Part II). · 0e8d7946
  Leon-Charles Tranchevent authored Feb 21, 2020
  
  0e8d7946
20 Feb, 2020 1 commit
- Enhanced step 08 - GRN (to run on iris / extended comments and documentation). · 2cbe8efb
  Leon-Charles Tranchevent authored Feb 20, 2020
  
  2cbe8efb
19 Feb, 2020 3 commits
- RNA-seq data integration (Part I). · 4ddae3a7
  Leon-Charles Tranchevent authored Feb 19, 2020
  
  4ddae3a7
- Few tweaks to run the code on Iris. · 0efc368f
  Leon-Charles Tranchevent authored Feb 19, 2020
  
  0efc368f
- New generic Makefile commands to synchronize the code / library / data. · 2c97a2d6
  Leon-Charles Tranchevent authored Feb 19, 2020
  
  2c97a2d6
18 Feb, 2020 3 commits
- Replaced usage of R library rowr (not supported any more). · 331b0628
  Leon-Charles Tranchevent authored Feb 18, 2020
  
  331b0628
- Changed the R module load commands after the last IRIS update. · 2364b348
  Leon-Charles Tranchevent authored Feb 18, 2020
  
  2364b348
- Enriched support for RNAseq datasets (limma / gene annotations). · 0c94a88e
  Leon-Charles Tranchevent authored Feb 18, 2020
  
  0c94a88e
14 Feb, 2020 1 commit
- Added support for preprocessed RNA-seq dataset (only NBB so far). · c9839b60
  Leon-Charles Tranchevent authored Feb 14, 2020
  
  c9839b60
31 Jan, 2020 1 commit
- DoRothEA / GeneGO analysis enhanced (matching, refining, overlap). · 765c19e7
  Leon-Charles Tranchevent authored Jan 31, 2020
  
  765c19e7
24 Jan, 2020 1 commit
- DoRothEa enrichment added / fine-tunning of gene name matching. · 841a30d1
  Leon-Charles Tranchevent authored Jan 24, 2020
  
  841a30d1
17 Jan, 2020 1 commit
- GeneGO and DoRothEA analyses added (step 08). · 1d7210ba
  Leon-Charles Tranchevent authored Jan 17, 2020
  
  1d7210ba
20 Dec, 2019 1 commit
- New integration strategy using a confidence score. · 746ca8cf
  Leon-Charles Tranchevent authored Dec 20, 2019
  
  746ca8cf
11 Dec, 2019 1 commit
- R scripts to generate enhanced figures (for presentation) added. · 2e2c6df9
  Leon-Charles Tranchevent authored Dec 11, 2019
  
  2e2c6df9
22 Nov, 2019 1 commit
- Gender specific pathway strategy implemented. · f7113b31
  Leon-Charles Tranchevent authored Nov 22, 2019
  
  f7113b31
15 Nov, 2019 1 commit
- New enrichment procedure (using 4 tools). · 81f27c62
  Leon-Charles Tranchevent authored Nov 15, 2019
  
  81f27c62
08 Nov, 2019 1 commit
- Some more adaptation in Best-Pval. Implementation of the subtract ranking strategy. · 96ae238c
  Leon-Charles Tranchevent authored Nov 08, 2019
  
  96ae238c
25 Oct, 2019 1 commit
- Few adaptations in the gene-probe method termed Best-Pval. Start to refactor step 07. · 5c427696
  Leon-Charles Tranchevent authored Oct 25, 2019
  
  5c427696
22 Oct, 2019 1 commit
- Small correction on the gene-probe selection method. · 463735db
  Leon-Charles Tranchevent authored Oct 22, 2019
  
  463735db
17 Oct, 2019 1 commit
- Adaptation of step 06 to the new configuration (2nd half). · fa8ebdeb
  Leon-Charles Tranchevent authored Oct 17, 2019
  
  fa8ebdeb
10 Oct, 2019 1 commit
- Code refactoring (VSN configuration / optimization / cleaning). · 94852040
  Leon-Charles Tranchevent authored Oct 10, 2019
  
  94852040
04 Oct, 2019 1 commit
- Adaptation of step 06 to the new configuration (1st half). · 4415e972
  Leon-Charles Tranchevent authored Oct 04, 2019
  
  4415e972
01 Oct, 2019 1 commit
- Added the APT-GCRMA preprocessing scripts, plus some refactoring for steps 01-04. · c726767e
  Leon-Charles Tranchevent authored Oct 01, 2019
  
  c726767e
27 Sep, 2019 1 commit
- Adaptation to new version of ArrayLibs (bug inversion bc / no bc). · 6a8dbf82
  Leon-Charles Tranchevent authored Sep 27, 2019
  
  6a8dbf82
24 Sep, 2019 1 commit
- New limma configuration and parameters. · 4daf7830
  Leon-Charles Tranchevent authored Sep 24, 2019
  
  4daf7830
23 Sep, 2019 1 commit
- Cleaner code for data pre-processing / cleaning / checking. · fc6d5374
  Leon-Charles Tranchevent authored Sep 23, 2019
  
  fc6d5374
20 Sep, 2019 1 commit
- Adapted the cleaning step / best processing method. · 49b5009f
  Leon-Charles Tranchevent authored Sep 20, 2019
  
  49b5009f
19 Sep, 2019 1 commit
- More tunable vsn method (parameters, input data). · 6c0129a7
  Leon-Charles Tranchevent authored Sep 19, 2019
  
  6c0129a7
18 Sep, 2019 2 commits
- Improved VSN method, added figures and LaTeX document. · d0c819c6
  Leon-Charles Tranchevent authored Sep 18, 2019
  
  d0c819c6
- Include the stabilizing variance function in the process (after pre-processing). · 7c3db6af
  Leon-Charles Tranchevent authored Sep 18, 2019
  
  7c3db6af
16 Sep, 2019 1 commit
- Added another dataset (GSE49036). · adefea86
  Leon-Charles Tranchevent authored Sep 16, 2019
  
  adefea86
08 Aug, 2019 1 commit
- Some refactoring, better logs, improved GC / meme usage. · 8eae268e
  Leon-Charles Tranchevent authored Aug 08, 2019
  
  8eae268e