Commits · c382d13d7fc6ee00fc111c4d9ff236a9ae1cbae2 · Matej Lexa / hic-te · GitLab

Sep 08, 2021
- Added an idea for plotting centromeres in BAMCoverage plots · c382d13d
  Matej Lexa authored Sep 08, 2021
  
  c382d13d
- Updated rice centromere position data acc to NAture paper from 2005 (coordinates still valid?) · d8914d56
  Matej Lexa authored Sep 08, 2021
  
  d8914d56
- Created a data folder for various distributed data files, starting with... · d4f0d280
  Matej Lexa authored Sep 08, 2021
```
Created a data folder for various distributed data files, starting with centromere positions to use with karyotypeR BAM plots
```
  d4f0d280
- Merge branch 'master' of https://gitlab.fi.muni.cz/lexa/hic-te · 1aaae698
  Matej Lexa authored Sep 08, 2021
  
  1aaae698
- Fixed a problem of failing when no heteronymic pairs were present · e3516e04
  Matej Lexa authored Sep 08, 2021
  
  e3516e04
- Remove unneeded argument from GENERATE_TABLE, ... · a25a5071
  Son Hoang Nguyen authored Sep 08, 2021
```
Make variable names more descriptive
```
  a25a5071
- Fix output name in intersect_bed.nf · 7ea217b7
  Son Hoang Nguyen authored Sep 08, 2021
  
  7ea217b7
- Update test profile, ... · fd84cd86
  Son Hoang Nguyen authored Sep 08, 2021
```
Modify SHUFFLE_FRAGMENTS to accept genome lenght.
Move process for generating table to its own module.
Add circos to main_TE_2.nf.
```
  fd84cd86
- Tested on hardcoded BAM files · ee3e2efc
  Matej Lexa authored Sep 08, 2021
  
  ee3e2efc
- Fixed output redirection error. · ee5e75fe
  Matej Lexa authored Sep 08, 2021
  
  ee5e75fe
- Initial commit for a script to plot BAM file genome coverage · 068e6fbe
  Matej Lexa authored Sep 08, 2021
  
  068e6fbe
Sep 07, 2021
- Initial commit for GENERATE_CHRLEN and SHUFFLE_FRAGMENTS as new blocks · a90c4faa
  Matej Lexa authored Sep 07, 2021
  
  a90c4faa
- convert positions into numeric values, add brackets for clarity · 606f33c8
  Monika Čechová authored Sep 07, 2021
  
  606f33c8
- format heatmap; order the table with p-values by the frequency of contactes in decreasing order · 0b111c20
  Monika Čechová authored Sep 07, 2021
  
  0b111c20
- Fixed TEHeatmap.R t accept new input tab format · 93c29146
  Matej Lexa authored Sep 07, 2021
  
  93c29146
- Fixed a typo in calling intersect_bed (missing t) · 465e6e90
  Matej Lexa authored Sep 07, 2021
  
  465e6e90
Sep 06, 2021
- added few comments · ac325e59
  Monika Čechová authored Sep 06, 2021
  
  ac325e59
- pairs of families that are significant are now written into the file · 76e13898
  Monika Čechová authored Sep 06, 2021
  
  76e13898
- rename to match the agreed format of the .tab file; limit the circos plots to 500 lines per plot · 1850f506
  Monika Čechová authored Sep 06, 2021
  
  1850f506
- create the index of the genome only if it does not exist yet · 2844dd37
  Monika Čechová authored Sep 06, 2021
  
  2844dd37
- Update circos.nf · caa63315
  Monika Čechová authored Sep 06, 2021
  
  caa63315
Sep 05, 2021
- Fixed an error of shuffling also experimental dataset that should have stayed unshuffled · 80bbb63a
  Matej Lexa authored Sep 05, 2021
  
  80bbb63a
- Convert 'TE to heatmap' to dsl2, add modules · 82c97d7e
  Son Hoang Nguyen authored Sep 05, 2021
  
  82c97d7e
Sep 02, 2021
- Update test.config · a942a859
  Son Hoang Nguyen authored Sep 02, 2021
  
  a942a859
- Add test profile, update main_TE_combined.nf with skip parameters · eee446e5
  Son Hoang Nguyen authored Sep 02, 2021
  
  eee446e5
- Modified ggplot calls to show title and axis labels · f7ce1b60
  Matej Lexa authored Sep 02, 2021
  
  f7ce1b60
- Added all steps of shuffledNormalization (bash + R) · 96a849e9
  Matej Lexa authored Sep 02, 2021
  
  96a849e9
- Fixed a bug when input contained an empty annot= variable · 5870c1df
  Matej Lexa authored Sep 02, 2021
  
  5870c1df
Sep 01, 2021
- adjusted regex in script to new tab format produced by extract_pairs.pl · 2f23f45b
  Matej Lexa authored Sep 01, 2021
  
  2f23f45b
- A format converter based on rtracklayer · 0b5a30ac
  Matej Lexa authored Sep 01, 2021
  
  0b5a30ac
- Changed pipeline to reflect changes in extract_pairs.pl · b719c2e0
  Matej Lexa authored Sep 01, 2021
  
  b719c2e0
- Adapted script to the new table format produced by extract_pairs.pl · d92dc881
  Matej Lexa authored Sep 01, 2021
  
  d92dc881
- Merge branch 'master' of https://gitlab.fi.muni.cz/lexa/hic-te · a2e98ce0
  Matej Lexa authored Sep 01, 2021
  
  a2e98ce0
- Modified script to produce a leaner table and accept distance limits · 7314c81c
  Matej Lexa authored Sep 01, 2021
  
  7314c81c
- Update plot_family_pairs.R · f3391ebc
  Monika Čechová authored Sep 01, 2021
  
  f3391ebc
- add process for the generation of genome file · c27cde37
  Monika Čechová authored Sep 01, 2021
  
  c27cde37
- automatically generate genome file for circos plots · 283275ba
  Monika Čechová authored Sep 01, 2021
  
  283275ba
- specify number of output reads · 5a96f915
  Monika Čechová authored Sep 01, 2021
  
  5a96f915
- specify number of output reads · fff1945a
  Monika Čechová authored Sep 01, 2021
  
  fff1945a
- Initial commit of new R script · dcc612da
  Matej Lexa authored Sep 01, 2021
  
  dcc612da