Commits · master · BDS / GeneDER / GeneDER_core

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 5 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
- Updated license file name for PPC. · 33e40008
  Leon-Charles Tranchevent authored Nov 23, 2021
  
  33e40008
12 Nov, 2021 2 commits
- Merge branch 'develop' into 'master' · 3bf5aec2
  Leon-Charles Tranchevent authored Nov 12, 2021
```
Modifications related to PPC.

See merge request bds/geneder/geneder!2
```
  3bf5aec2
- Changed some comments that were understood by cylon-x as statements about licenses. · 8f57bd4b
  Leon-Charles Tranchevent authored Nov 12, 2021
  
  8f57bd4b
11 Nov, 2021 5 commits
- Merge branch 'develop' into 'master' · 03452f7f
  Leon-Charles Tranchevent authored Nov 11, 2021
```
Updated pipeline for manuscript submission.

See merge request bds/geneder/geneder!1
```
  03452f7f
- Modified enrichment procedure to take into account gene sets with very few genes. · 6ede0b4c
  Leon-Charles Tranchevent authored Nov 11, 2021
  
  6ede0b4c
- Updated README with latest manuscript details. · 57624928
  Leon-Charles Tranchevent authored Nov 11, 2021
  
  57624928
- New method to plot the cell type biomarkers per dataset. · 3c574ea8
  Leon-Charles Tranchevent authored Nov 11, 2021
  
  3c574ea8
- Corrected garbage collection. · 5be415ac
  Leon-Charles Tranchevent authored Nov 11, 2021
  
  5be415ac
13 Oct, 2021 1 commit
- Updated scRNA-seq analysis pipeline. · f293ccca
  Leon-Charles Tranchevent authored Oct 13, 2021
  
  f293ccca
03 Sep, 2021 1 commit
- First version of the scRNA-seq analysis pipeline (up until differential expression). · fd93d4c9
  Leon-Charles Tranchevent authored Sep 03, 2021
  
  fd93d4c9
05 May, 2021 1 commit
- New manuscript title. · 7ecb2460
  Leon-Charles Tranchevent authored May 05, 2021
  
  7ecb2460
16 Mar, 2021 3 commits
- Merge branch 'develop' into 'master'. · 1ae85b89
  Leon-Charles Tranchevent authored Mar 16, 2021
  
  1ae85b89
- Added MIT license. · f26f07fa
  Leon-Charles Tranchevent authored Mar 16, 2021
  
  f26f07fa
- Updated README file · 76f7b571
  Leon-Charles Tranchevent authored Mar 16, 2021
  
  76f7b571
15 Mar, 2021 2 commits
- Coding style harmonized. · 9527d599
  Leon-Charles Tranchevent authored Mar 15, 2021
  
  9527d599
- Updated README files. · bbf6a822
  Leon-Charles Tranchevent authored Mar 15, 2021
  
  bbf6a822
08 Mar, 2021 2 commits
- Refactoring step 08 in agreement with the latest changes in the overall workflow. · 8bcecb01
  Leon-Charles Tranchevent authored Mar 08, 2021
  
  8bcecb01
- Cosmetic changes to the integration step. · fbfefcbd
  Leon-Charles Tranchevent authored Mar 08, 2021
  
  fbfefcbd
21 Dec, 2020 1 commit
- Refined the gender specific pathway figures. · 3e4e2db5
  Leon-Charles Tranchevent authored Dec 21, 2020
  
  3e4e2db5
28 Nov, 2020 3 commits
- Few adjustment for gene figures (both for top hits and selected genes). · 84aa8519
  Leon-Charles Tranchevent authored Nov 28, 2020
  
  84aa8519
- Correcting typo in GEO bash variable name. · 0ef244af
  Leon-Charles Tranchevent authored Nov 28, 2020
  
  0ef244af
- Refactoring step 07 to process all datasets at once (Part I). · aaf736be
  Leon-Charles Tranchevent authored Nov 28, 2020
  
  aaf736be
24 Nov, 2020 1 commit
- Refactoring step 06 to process all datasets at once (Part III). · 69511fa6
  Leon-Charles Tranchevent authored Nov 24, 2020
  
  69511fa6
20 Nov, 2020 1 commit
- Refactoring step 06 to process all datasets at once (Part II). · d3a82871
  Leon-Charles Tranchevent authored Nov 20, 2020
  
  d3a82871
18 Nov, 2020 1 commit
- Minor modifications in step 06 to optimize the code (duplicate_rows). · 77f8c71f
  Leon-Charles Tranchevent authored Nov 18, 2020
  
  77f8c71f
13 Nov, 2020 1 commit
- Refactoring step 06 to process all datasets at once. · fe85f14c
  Leon-Charles Tranchevent authored Nov 13, 2020
  
  fe85f14c
12 Nov, 2020 1 commit
- Refactoring step 05 to process all datasets at once. · 96c62eee
  Leon-Charles Tranchevent authored Nov 12, 2020
  
  96c62eee
11 Nov, 2020 1 commit
- Refactoring step 04 to process all datasets at once (Second part - after match). · a42c7580
  Leon-Charles Tranchevent authored Nov 11, 2020
  
  a42c7580
10 Nov, 2020 1 commit
- Refactoring step 04 to process all datasets at once (First part - until match) · f2e78969
  Leon-Charles Tranchevent authored Nov 10, 2020
  
  f2e78969
08 Nov, 2020 1 commit
- Refactoring step 03 to process all datasets at once (microarray and RNA-seq). · 9b1ebb03
  Leon-Charles Tranchevent authored Nov 08, 2020
  
  9b1ebb03
04 Nov, 2020 1 commit
- Small modifications to steps 01 and 02 (wrt a bug for the RNA-seq datasets and... · 20994b82
  Leon-Charles Tranchevent authored Nov 04, 2020
```
Small modifications to steps 01 and 02 (wrt a bug for the RNA-seq datasets and the new QOS on iris).
```
  20994b82
28 Oct, 2020 1 commit
- Refactoring steps 01 and 02 to process all datasets at once (microarray and RNA-seq). · 58c4002c
  Leon-Charles Tranchevent authored Oct 28, 2020
  
  58c4002c
21 Oct, 2020 2 commits
- Code refactoring and optimization for th second step (RNA-seq and array... · 8b38640b
  Leon-Charles Tranchevent authored Oct 21, 2020
```
Code refactoring and optimization for th second step (RNA-seq and array datasets are now processed altogether).
```
  8b38640b
- Code refactoring and optimization for step 01. · 892ed6fc
  Leon-Charles Tranchevent authored Oct 21, 2020
  
  892ed6fc
09 Oct, 2020 1 commit
- Added the code to create gene expression heatmaps and modified the code that... · a07ae9cd
  Leon-Charles Tranchevent authored Oct 09, 2020
```
Added the code to create gene expression heatmaps and modified the code that creates the pathway visualizations.
```
  a07ae9cd