Commits · master · Zhang, Jennings / ttt13309

Dec 14, 2020
- Normalize tp to T0, T1, T2, extract snp_reshape.py input glob · 9bbbee96
  Jennings Zhang authored 4 years ago
  
  9bbbee96
- 🍉 · 43ced38b
  Jennings Zhang authored 4 years ago
  
  43ced38b
Oct 20, 2020
- Update hardcoded paths and remove duplicate code · 742d85f1
  Jennings Zhang authored 4 years ago
  
  742d85f1
- Use driver file basename · bd35dbe4
  Zhang, Jennings authored 4 years ago
  
  bd35dbe4
- Update README.md · 3bacea21
  Zhang, Jennings authored 4 years ago
  
  3bacea21
- Fix relapse timepoints · 4c01963e
  Zhang, Jennings authored 4 years ago
  
  4c01963e
- Update README.md · 2e6280cf
  Zhang, Jennings authored 4 years ago
  
  2e6280cf
- Update README.md · d743d840
  Zhang, Jennings authored 4 years ago
  
  d743d840
Oct 15, 2020
- Use groupby · 374cd26a
  Jennings Zhang authored 4 years ago
  
  374cd26a
- Ishwarya's one file format · d1644915
  Jennings Zhang authored 4 years ago
  
  d1644915
- Capitalize README · 8612597b
  Jennings Zhang authored 4 years ago
  
  8612597b
Oct 08, 2020
- Add Event_Name to cnv result output · ba2140e5
  Zhang, Jennings authored 4 years ago
  
  ba2140e5
- Fix save duplicate uncombinable · 01243e45
  Zhang, Jennings authored 4 years ago
  
  01243e45
- cnv_organize.py · 30397ee9
  Zhang, Jennings authored 4 years ago
  
  30397ee9
- Fix 2-way overlap condition · 93b00436
  Zhang, Jennings authored 4 years ago
  
  93b00436
- Fix repeat recusion, fix merged name collision · ee8d93d7
  Zhang, Jennings authored 4 years ago
  
  ee8d93d7
- Change warning_log/ to needs_review/ · 8d2ceec7
  Zhang, Jennings authored 4 years ago
  
  8d2ceec7
- Fix 2of3 combinable but not combined · 1ed53808
  Zhang, Jennings authored 4 years ago
  
  1ed53808
Sep 23, 2020
- Combine overlapping cnv · 357ee044
  Zhang, Jennings authored 4 years ago
  
  357ee044
Sep 09, 2020
- Increasing clonal · 478d16a7
  Zhang, Jennings authored 4 years ago
  
  478d16a7
- Split download and reshaping · db1880cc
  Zhang, Jennings authored 4 years ago
  
  db1880cc
Sep 08, 2020
- Low reads QC · 124b86ab
  Zhang, Jennings authored 4 years ago
  
  124b86ab
- Rerun notebooks, add Patient_ID to freq_table · 9413919a
  Zhang, Jennings authored 4 years ago
  
  9413919a
- Exclude clonal · 0972316b
  Zhang, Jennings authored 4 years ago
  
  0972316b
Sep 03, 2020
- Separate consolidated table by driver · 5a3deafb
  Zhang, Jennings authored 4 years ago
  
  5a3deafb
- Move off JBrown shared drive · 30058015
  Zhang, Jennings authored 4 years ago
  
  30058015
- Add lineplot · 4fd2826e
  Zhang, Jennings authored 4 years ago
  
  4fd2826e
- Replace unknown Protein_change w/ Start_position · e7141e57
  Zhang, Jennings authored 4 years ago
  
  e7141e57
- Oops py vars · 975e5101
  Zhang, Jennings authored 4 years ago
  
  975e5101
- Write mutation names to all_patients.tsv · 0c3b7ada
  Zhang, Jennings authored 4 years ago
  
  0c3b7ada
- More detailed organize output · cc00a7d7
  Zhang, Jennings authored 4 years ago
  
  cc00a7d7
Sep 02, 2020
- List genes decreasing during both remission and relapse · 674b61e3
  Zhang, Jennings authored 4 years ago
  
  674b61e3
- Details freq analysis results · d97e3643
  Zhang, Jennings authored 4 years ago
  
  d97e3643
Aug 27, 2020
- Organize outputs · 5515c436
  Zhang, Jennings authored 4 years ago
  
  5515c436
Aug 25, 2020
- Use df.set_index instead of df.index = · db6ad381
  Zhang, Jennings authored 4 years ago
  
  db6ad381
- Float format output to individual patient files · ffc764bf
  Zhang, Jennings authored 4 years ago
  
  ffc764bf
- Drop gene info columns · 965b701e
  Zhang, Jennings authored 4 years ago
```
These can be read back in by cross-referencing source data.
```
  965b701e
- Preserve allele count info · 66ef30c0
  Zhang, Jennings authored 4 years ago
  
  66ef30c0
- Keep Patient_ID too · 072bdd2b
  Zhang, Jennings authored 4 years ago
  
  072bdd2b
- Deprecate thresholding and mark important · b5ca95bd
  Zhang, Jennings authored 4 years ago
  
  b5ca95bd