Commits · master · Blaise LI / libcodonusage

12 Dec, 2022 1 commit
- Try to fix detection of clustering diffs. · d1cb929b
  Blaise Li authored Dec 12, 2022
  
  d1cb929b
02 May, 2022 1 commit
- Optional codon influence in PCA. · 7b63a9e2
  Blaise Li authored May 02, 2022
  
  7b63a9e2
29 Apr, 2022 2 commits
- More easy to choose fig formats. · e6f55702
  Blaise Li authored Apr 29, 2022
  
  e6f55702
- Option to exclude columns for PCA. · 64894825
  Blaise Li authored Apr 29, 2022
  
  64894825
28 Apr, 2022 2 commits
- Start fixing aa usage violin plots. · 6530db56
  Blaise Li authored Apr 28, 2022
  
  6530db56
- PCA, filtering by chromosome. · b37e7ce5
  Blaise Li authored Apr 28, 2022
  
  b37e7ce5
14 Apr, 2022 3 commits
- More output from bias-calculating functions. · efd54b2d
  Blaise Li authored Apr 14, 2022
  
  efd54b2d
- Option to return proportions too, not just biases. · ad2d5a2e
  Blaise Li authored Apr 14, 2022
  
  ad2d5a2e
- Mention references. · c8e29f65
  Blaise Li authored Apr 14, 2022
  
  c8e29f65
12 Apr, 2022 1 commit
- Figure size tweaks, violins by chromosome. · 8ca17aef
  Blaise Li authored Apr 12, 2022
  
  8ca17aef
11 Apr, 2022 1 commit
- Further forward violin plot kwargs. · b2ea4106
  Blaise Li authored Apr 11, 2022
  
  b2ea4106
07 Apr, 2022 2 commits
- Forward arguments to violin plot. · 14de21d2
  Blaise Li authored Apr 07, 2022
  
  14de21d2
- Fix aa and codon order, better long form. · 6b3bb11b
  Blaise Li authored Apr 07, 2022
  
  6b3bb11b
05 Apr, 2022 1 commit
- Fix violin order. Legend issues. · 189af8b9
  Blaise Li authored Apr 05, 2022
  
  189af8b9
25 Mar, 2022 1 commit
- Function to compare clusterings. · 437a43ec
  Blaise Li authored Mar 25, 2022
  
  437a43ec
24 Mar, 2022 2 commits
- Allow imprecision in global codon proportions sum. · b046962e
  Blaise Li authored Mar 24, 2022
  
  b046962e
- Allow custom info columns in counts table. · 3fbb71e9
  Blaise Li authored Mar 24, 2022
  
  3fbb71e9
23 Mar, 2022 1 commit
- Gene extraction and plotting functions. · 4f5b9211
  Blaise Li authored Mar 23, 2022
  
  4f5b9211
18 Mar, 2022 1 commit
- Threshold finding function. · ae4349e4
  Blaise Li authored Mar 18, 2022
  
  ae4349e4
17 Mar, 2022 2 commits
- Function to write genes list from clusters. · 598c606d
  Blaise Li authored Mar 17, 2022
  
  598c606d
- Functions to cluster around "full-bias" centroids. · 80d5d3ae
  Blaise Li authored Mar 17, 2022
  
  80d5d3ae
15 Mar, 2022 1 commit
- Computation of cluster centroids. · e486cb54
  Blaise Li authored Mar 15, 2022
  
  e486cb54
14 Mar, 2022 3 commits
- Function to exclude columns with only NaNs. · 3b410576
  Blaise Li authored Mar 14, 2022
  
  3b410576
- Function computing aa usage biases. · a602b0bf
  Blaise Li authored Mar 14, 2022
  
  a602b0bf
- Functions to compute usage biases. · 57e7c060
  Blaise Li authored Mar 14, 2022
  
  57e7c060
09 Mar, 2022 1 commit
- Handle new input and border cases. · fa1283b6
  Blaise Li authored Mar 09, 2022
  
  fa1283b6
04 Mar, 2022 3 commits
- Fixed column order, nicer output. · 0390d53d
  Blaise Li authored Mar 04, 2022
  
  0390d53d
- Added function to group counts columns by aa. · cf468c0f
  Blaise Li authored Mar 04, 2022
  
  cf468c0f
- Reorganize code. · 0ea7c404
  Blaise Li authored Mar 04, 2022
  
  0ea7c404
02 Mar, 2022 3 commits
- Counts table reformatting. · 6a808558
  Blaise Li authored Mar 02, 2022
  
  6a808558
- More potential selection criteria for genes. · a85cbad9
  Blaise Li authored Mar 02, 2022
  
  a85cbad9
- Code to run diagnostics about genes. · 705a8246
  Blaise Li authored Mar 02, 2022
  
  705a8246
25 Feb, 2022 1 commit
- Add markdown rendered for Jupyter notebook. · f43bdd71
  Blaise Li authored Feb 25, 2022
  
  f43bdd71
02 Feb, 2022 1 commit
- Made a separate libcodonusage library. · afe708f0
  Blaise Li authored Feb 02, 2022
```
See https://stackoverflow.com/a/17864475/1878788
```
  afe708f0
19 Jan, 2022 1 commit
- Added top 25% gene lists. · 623b0307
  Blaise Li authored Jan 19, 2022
  
  623b0307
18 Jan, 2022 1 commit
- Set seed, table loading in library, re-run. · 77ea577f
  Blaise Li authored Jan 18, 2022
  
  77ea577f
21 Jul, 2021 2 commits
- Gene list extraction in separate notebook. · df6c8c63
  Blaise Li authored Jul 21, 2021
  
  df6c8c63
- Moving some code to a common module. · 2c1de339
  Blaise Li authored Jul 21, 2021
```
The goal is to split the Explore_usage_biases.ipynb notebook in two.
```
  2c1de339