Commits · dev · Matej Lexa / hic-te · GitLab

Nov 02, 2023
- Update singularity & docker containers · 345e1b6c
  Son Hoang Nguyen authored Nov 02, 2023
  
  345e1b6c
Oct 26, 2022
- Allow custom arg for BBMap tools · 262cd528
  Son Hoang Nguyen authored Oct 26, 2022
  
  262cd528
Oct 25, 2022
- Allow custom cpu/thread arg values for some tools · fb1d8bcb
  Son Hoang Nguyen authored Oct 25, 2022
  
  fb1d8bcb
Oct 21, 2022
- Merge branch 'master' into dev · 578ace74
  Son Hoang Nguyen authored Oct 21, 2022
  
  578ace74
Oct 20, 2022
- Use default OS java instead of forcing java 8 · 80af94f3
  Son Hoang Nguyen authored Oct 20, 2022
  
  80af94f3
- Add parameter publish_dir_mode · 2b1e7675
  Son Hoang Nguyen authored Oct 20, 2022
  
  2b1e7675
Oct 18, 2022
- Choice between RM and TE-nester added · 8ff7320d
  Matej Lexa authored Oct 18, 2022
  
  8ff7320d
- Fixed R script that complaint when no contigs were blasted and file had size zero · fe74dade
  Matej Lexa authored Oct 18, 2022
  
  fe74dade
- Fixed annotate_exons module grep problem, added promoters and enhancers to the pattern · 3df6c649
  Matej Lexa authored Oct 18, 2022
  
  3df6c649
- Fixed annotate_exons module grep problem · 525de20f
  Matej Lexa authored Oct 18, 2022
  
  525de20f
- Fied nextflow.config for human.config · c9ad6876
  Matej Lexa authored Oct 18, 2022
  
  c9ad6876
- Merge branch 'master' of https://gitlab.fi.muni.cz/lexa/hic-te · 9a3b9a47
  Matej Lexa authored Oct 18, 2022
  
  9a3b9a47
- Added human config · 0d8b04fc
  Matej Lexa authored Oct 18, 2022
  
  0d8b04fc
Oct 14, 2022
- Add singularity containers for rtools, nester · 2fab1506
  Son Hoang Nguyen authored Oct 14, 2022
  
  2fab1506
Oct 12, 2022
- added promoters and enhancers to annotate_exons.nf · 1c833f6f
  Matej Lexa authored Oct 12, 2022
  
  1c833f6f
Sep 18, 2022
- modify: changelog · b03c41ab
  Matej authored Sep 18, 2022
  
  b03c41ab
- add: betools window, modify: typo lenght -> length · 55636b90
  Matej authored Sep 18, 2022
  
  55636b90
Aug 17, 2022
- modify: pass common.R file as parameter · e965b1e4
  Matej authored Aug 17, 2022
  
  e965b1e4
Aug 06, 2022
- modify: shared R functions in separate file · 95c7c7ab
  Matej authored Aug 06, 2022
  
  95c7c7ab
Aug 02, 2022
- introduce: changelog · 55eec84d
  Matej authored Aug 02, 2022
  
  55eec84d
Jul 31, 2022
- fixed skip_sra · 5baee68f
  Matej Lexa authored Jul 31, 2022
  
  5baee68f
Jun 09, 2022
- Added empty variables for Repeat Masker option to test.config · e3e744ce
  Matej Lexa authored Jun 09, 2022
  
  e3e744ce
- Added and tested repeat masker option on Arabidopsis · 6e2c0ca5
  Matej Lexa authored Jun 09, 2022
  
  6e2c0ca5
Jun 07, 2022
- Added Repeat Masker notes and extra heatmap visualization parameters after manuscript revision · 52eac3cb
  Matej Lexa authored Jun 07, 2022
  
  52eac3cb
Jun 02, 2022
- Fixed a typo in the string reference_free that prevented printing heatmap correctly · 6511372f
  Matej Lexa authored Jun 02, 2022
  
  6511372f
- fixed bug in setting limit_count in heatmap plotting · e1368765
  Matej Lexa authored Jun 02, 2022
  
  e1368765
- Lowere limit count from 50 to 30 and set it to 0 for reference-free · edf114fc
  Matej Lexa authored Jun 02, 2022
  
  edf114fc
- Fixed a bug in bash skript choosing execution between nester and repeat masker · eea39377
  Matej Lexa authored Jun 02, 2022
  
  eea39377
Jun 01, 2022
- Added statistical graying of heatmaps by two parameters for minimal read count and normalized ratio · 489948f4
  Matej Lexa authored Jun 01, 2022
  
  489948f4
May 30, 2022
- A script to import RepeatMasker output · b45a6edc
  Matej Lexa authored May 30, 2022
  
  b45a6edc
May 19, 2022
- Added a description of the counting procedure · 3a12d251
  Matej Lexa authored May 19, 2022
  
  3a12d251
Apr 20, 2022
- Update nester docker container · 590996c9
  Son Hoang Nguyen authored Apr 20, 2022
  
  590996c9
Apr 14, 2022
- added labels for track (family1 and family2), both families plotted separately now · 0c99590a
  Monika Čechová authored Apr 14, 2022
  
  0c99590a
- Merge branch 'develop' into 'master' · caa21d6f
  Matej Lexa authored Apr 14, 2022
```
Develop

See merge request !1
```
  caa21d6f
- Circos: gene densities and subsets of repeats are now plotted whenever possible. · dddb7240
  Monika authored Apr 14, 2022
  
  dddb7240
Mar 30, 2022
- Circos now plots gene track. · ffab3b2d
  Monika authored Mar 30, 2022
  
  ffab3b2d
Mar 21, 2022
- Update Diachromatic.jar · 3bcaa3d9
  Son Hoang Nguyen authored Mar 21, 2022
  
  3bcaa3d9
Mar 19, 2022
- Add files for building docker image for rtools · d71b3c1d
  Son Hoang Nguyen authored Mar 19, 2022
  
  d71b3c1d
Jan 04, 2022
- Fixed bin/R/plot_barplot.R to have wider margin below x-axis · 8ff15292
  Matej Lexa authored Jan 04, 2022
  
  8ff15292
- Improved plantSat.fa description · 5c99a833
  Matej Lexa authored Jan 04, 2022
  
  5c99a833