Commits · master · Emilien Lasguignes / intronSeeker

16 Jun, 2022 1 commit
- Remove xbins and add yaxis and xaxis range to plot_hist to display the number... · cab39181
  Sarah Maman-Haddad authored Jun 16, 2022
```
Remove xbins and add yaxis and xaxis range to plot_hist to display the number of reads per length range
```
  cab39181
06 Jan, 2022 1 commit
- Check HiSat2 indexing and add process logs · af1baaeb
  SarahMaman authored Jan 06, 2022
  
  af1baaeb
05 Jan, 2022 1 commit
- Check HiSat2 indexing and add process logs · 2a9eb12c
  SarahMaman authored Jan 05, 2022
  
  2a9eb12c
20 Dec, 2021 1 commit
- Update dependencies · 92ddaed8
  Philippe Bardou authored Dec 20, 2021
  
  92ddaed8
15 Jul, 2021 1 commit
- Update simulation2HTML.py to comment SYNTHESE.csv file · bf7cfe13
  Sarah Maman-Haddad authored Jul 15, 2021
  
  bf7cfe13
13 Jul, 2021 2 commits
- GTF file optional for real data · 74cd5d03
  Sarah Maman authored Jul 13, 2021
  
  74cd5d03
- Remove GTF graphs for real data · a0e15d0e
  Sarah Maman authored Jul 13, 2021
  
  a0e15d0e
12 Jul, 2021 1 commit
- Update simulation2HTMLparse.py to add DP_before, DP_in and DP_after cols in df_candidat. · 759b4abd
  Sarah Maman-Haddad authored Jul 12, 2021
  
  759b4abd
02 Jul, 2021 1 commit
- DP before/in/after candidate and keyword DPR in filter field · 71950467
  Philippe Bardou authored Jul 02, 2021
  
  71950467
29 Jun, 2021 1 commit
- Find evidence - score v1 · 15981f9a
  Philippe Bardou authored Jun 29, 2021
  
  15981f9a
23 Feb, 2021 1 commit
- Modify report html name : "_simulation.html" replaced by ".html" in order to... · 882f69c2
  Sarah Maman-Haddad authored Feb 23, 2021
```
Modify report html name : "_simulation.html" replaced by ".html" in order to take real cases into account.
```
  882f69c2
10 Feb, 2021 1 commit
- Merge analyze ORF and Prot · 8d59a698
  Philippe Bardou authored Feb 10, 2021
  
  8d59a698
09 Feb, 2021 1 commit
- Convert df.contig in string when it is in int format in some GTF files (as... · 49bc361f
  Sarah Maman-Haddad authored Feb 09, 2021
```
Convert df.contig in string when it is in int format in some GTF files (as chicken Gallus_gallus.GRCg6a.102.gtf).
```
  49bc361f
08 Feb, 2021 1 commit
- (minor) separation of the code between real and simulated cases · c6ac0010
  Sarah Maman authored Feb 08, 2021
  
  c6ac0010
05 Feb, 2021 2 commits
- Mise en forme get_html_seq_descr (real/simulation cases) · 2f310e16
  Sarah Maman-Haddad authored Feb 05, 2021
  
  2f310e16
- Mise en forme get_html_seq_descr (real/simulation cases) · bdac9cc6
  Sarah Maman-Haddad authored Feb 05, 2021
  
  bdac9cc6
04 Feb, 2021 1 commit
- Add real cases in simulation2HTML scripts · 3353df8a
  Sarah Maman authored Feb 04, 2021
  
  3353df8a
01 Feb, 2021 2 commits
- Merge branch 'master' of forgemia.inra.fr:emilien.lasguignes/intronSeeker · 554599bc
  Philippe Bardou authored Feb 01, 2021
  
  554599bc
- AnalyseORF/Prot · b8f4ac43
  Philippe Bardou authored Feb 01, 2021
  
  b8f4ac43
19 Jan, 2021 1 commit
- Argument minfootsize at 10 by default in intronSeeker.py file. · d72cdc8e
  Sarah Maman-Haddad authored Jan 19, 2021
  
  d72cdc8e
08 Jan, 2021 1 commit
- Correction foot var in intronSearch.py · 441247e7
  Sarah Maman-Haddad authored Jan 08, 2021
  
  441247e7
06 Jan, 2021 1 commit
- Remove reads with foot < minfootsize in intronSearch.py file · ce971e8b
  Sarah Maman-Haddad authored Jan 06, 2021
  
  ce971e8b
11 Dec, 2020 3 commits
- Add an option for the filter on foot size - minor correction · 058d395d
  Sarah Maman authored Dec 11, 2020
  
  058d395d
- Add an option for the filter on foot size >= 5 in splitReadSearch search · fe5fc14b
  Sarah Maman authored Dec 11, 2020
  
  fe5fc14b
- Add a filter on foot size >= 5 in splitReadSearch search · 67ca97d8
  Sarah Maman authored Dec 11, 2020
  
  67ca97d8
10 Dec, 2020 3 commits
- (minor) Add if in removeTranscriptsComingFromSameGene function · 007bf19d
  Sarah Maman authored Dec 10, 2020
  
  007bf19d
- Add removeTranscriptsComingFromSameGene function · da8dc4e6
  Philippe Bardou authored Dec 10, 2020
  
  da8dc4e6
- Add u option in GBS data simulation · 69358e98
  Sarah Maman authored Dec 10, 2020
  
  69358e98
09 Dec, 2020 4 commits
- AnalyzeORF · 94cbd5a9
  Philippe Bardou authored Dec 09, 2020
  
  94cbd5a9
- Merge branch 'master' of forgemia.inra.fr:emilien.lasguignes/intronSeeker · ccdffd78
  Philippe Bardou authored Dec 09, 2020
  
  ccdffd78
- AnalyzeORF · 13454b12
  Philippe Bardou authored Dec 09, 2020
  
  13454b12
- Filter 'Top 10 of contigs with the highest number of detected introns' tab... · c6f37d0b
  Sarah Maman authored Dec 09, 2020
```
Filter 'Top 10 of contigs with the highest number of detected introns' tab with only PASS candidates
```
  c6f37d0b
04 Dec, 2020 1 commit
- comment writing of local SYNTHESE.csv file · 2a1c2a97
  Sarah Maman authored Dec 04, 2020
  
  2a1c2a97
01 Dec, 2020 1 commit
- modify criteria to detect overlapping retained intron in intronSearch.py · dba7c68b
  Sarah Maman authored Dec 01, 2020
  
  dba7c68b
13 Nov, 2020 1 commit
- read.mapping_quality >= 2 in SplitReadSearch step · ec9f354f
  Sarah Maman authored Nov 13, 2020
  
  ec9f354f
12 Nov, 2020 2 commits
- Bug FP - Recompute read pos on modified contig · d271b2b5
  Philippe Bardou authored Nov 12, 2020
  
  d271b2b5
- Bug FP - Recompute read pos on modified contig · c0786efc
  Philippe Bardou authored Nov 12, 2020
  
  c0786efc
10 Nov, 2020 1 commit
- Add to df_library the read positions on the modified contig · 90006a14
  Sarah Maman authored Nov 10, 2020
  
  90006a14
09 Nov, 2020 1 commit
- Try to correct reads positions · 695abd44
  Sarah Maman authored Nov 09, 2020
  
  695abd44
30 Oct, 2020 1 commit
- (minor)Add condition to filter FP in order to remove TP tagged as FP · 0cf7a355
  Sarah Maman authored Oct 30, 2020
  
  0cf7a355